PySSA.pyssa.presenter.main_presenter
Module for the main view presenter of the pyssa plugin.
1# 2# PySSA - Python-Plugin for Sequence-to-Structure Analysis 3# Copyright (C) 2022 4# Martin Urban (martin.urban@studmail.w-hs.de) 5# Hannah Kullik (hannah.kullik@studmail.w-hs.de) 6# 7# Source code is available at <https://github.com/urban233/PySSA> 8# 9# This program is free software: you can redistribute it and/or modify 10# it under the terms of the GNU General Public License as published by 11# the Free Software Foundation, either version 3 of the License, or 12# (at your option) any later version. 13# 14# This program is distributed in the hope that it will be useful, 15# but WITHOUT ANY WARRANTY; without even the implied warranty of 16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 17# GNU General Public License for more details. 18# 19# You should have received a copy of the GNU General Public License 20# along with this program. If not, see <http://www.gnu.org/licenses/>. 21# 22"""Module for the main view presenter of the pyssa plugin.""" 23import logging 24import os 25import shutil 26import subprocess 27import sys 28import pathlib 29import csv 30 31import numpy as np 32import pymol 33from typing import TYPE_CHECKING 34from pymol import cmd 35from PyQt5 import QtGui 36from PyQt5 import QtWidgets 37from PyQt5 import QtCore 38from PyQt5.QtCore import Qt 39 40from pyssa.gui.ui.dialogs import dialog_settings_global 41from pyssa.gui.ui.dialogs import dialog_help 42from pyssa.gui.ui.dialogs import dialog_startup 43from pyssa.gui.ui.dialogs import dialog_distance_histogram 44from pyssa.gui.ui.dialogs import dialog_about 45from pyssa.gui.ui.dialogs import dialog_advanced_prediction_configurations 46from pyssa.gui.ui.dialogs import dialog_tutorial_videos 47from pyssa.gui.ui.dialogs import dialog_rename_protein 48from pyssa.gui.ui.messageboxes import basic_boxes 49from pyssa.gui.ui.styles import styles 50from pyssa.gui.ui.views import plot_view, add_protein_view 51 52from pyssa.internal.data_structures import protein 53from pyssa.internal.data_structures import project 54from pyssa.internal.data_structures import project_watcher 55from pyssa.internal.data_structures import settings 56from pyssa.internal.data_structures.data_classes import prediction_configuration, prediction_protein_info 57from pyssa.internal.data_structures.data_classes import image_state 58from pyssa.internal.data_structures.data_classes import stage 59from pyssa.internal.data_structures.data_classes import current_session 60from pyssa.internal.data_structures.data_classes import main_window_state 61from pyssa.internal.data_structures.data_classes import results_state 62from pyssa.internal.thread import task_workers, tasks 63 64from pyssa.io_pyssa import safeguard, filesystem_helpers 65from pyssa.io_pyssa import filesystem_io 66from pyssa.io_pyssa import path_util 67 68from pyssa.util import pyssa_keys, prediction_util 69from pyssa.util import main_window_util 70from pyssa.util import exit_codes 71from pyssa.util import globals 72from pyssa.util import session_util 73from pyssa.util import exception 74from pyssa.util import constants 75from pyssa.util import input_validator 76from pyssa.util import gui_page_management 77from pyssa.util import tools 78from pyssa.util import gui_utils 79from pyssa.logging_pyssa import log_handlers 80from pyssa.presenter import main_presenter_async 81 82if TYPE_CHECKING: 83 from pyssa.gui.ui.views import main_view 84 85logger = logging.getLogger(__file__) 86logger.addHandler(log_handlers.log_file_handler) 87 88 89class MainPresenter: 90 """Class for main presenter of the pyssa plugin.""" 91 92 """ 93 The main view of the pyssa plugin. 94 """ 95 _view: "main_view.MainView" 96 97 """ 98 The path to the active workspace. 99 """ 100 _workspace_path: pathlib.Path 101 102 """ 103 The application settings object. 104 """ 105 _application_settings: "settings.Settings" 106 107 """ 108 The currently active project. 109 """ 110 _current_project: "project.Project" 111 112 """ 113 A watcher for the project state. 114 """ 115 _project_watcher: "project_watcher.ProjectWatcher" 116 117 """ 118 The active task of the application. 119 """ 120 _active_task: tasks.Task 121 122 def __init__(self, a_view: "main_view.MainView") -> None: 123 """Constructor. 124 125 Args: 126 a_view: the main view of the pyssa plugin. 127 128 Raises: 129 IllegalArgumentException: If an argument is illegal. 130 """ 131 # <editor-fold desc="Checks"> 132 safeguard.Safeguard.check_if_value_is_not_none(a_view, logger) 133 134 # </editor-fold> 135 136 # <editor-fold desc="Initialize class attributes"> 137 self._view = a_view 138 self._workspace_path = constants.DEFAULT_WORKSPACE_PATH 139 # TODO: settings and project objects get not initialized properly 140 self._application_settings = settings.Settings("", "") 141 self._current_project: "project.Project" = project.Project() 142 self._project_watcher: "project_watcher.ProjectWatcher" = project_watcher.ProjectWatcher(self._current_project) 143 144 # </editor-fold> 145 146 # Check OS 147 main_window_util.check_operating_system() 148 # Create log dir 149 # <editor-fold desc="Program directory check"> 150 filesystem_helpers.create_directory(pathlib.Path(f"{os.path.expanduser('~')}/.pyssa")) 151 filesystem_helpers.create_directory(pathlib.Path(f"{os.path.expanduser('~')}/.pyssa/logs")) 152 constants.PYSSA_LOGGER.info("Checked program and logs directory.") 153 154 # </editor-fold> 155 # Configure settings 156 # <editor-fold desc="Setup App Settings"> 157 self._application_settings = settings.Settings(constants.SETTINGS_DIR, constants.SETTINGS_FILENAME) 158 if not os.path.exists(constants.SETTINGS_FULL_FILEPATH): 159 constants.PYSSA_LOGGER.info("Settings file not found, open configuration dialog.") 160 # Configuration dialog to setup setting file 161 dialog = dialog_startup.DialogStartup() 162 dialog.exec_() 163 164 # checks if the cancel button was pressed 165 if dialog_startup.global_var_terminate_app == 1: 166 os.remove(constants.SETTINGS_FULL_FILEPATH) 167 constants.PYSSA_LOGGER.info("Configuration dialog closed, and removed new settings file.") 168 sys.exit() 169 170 self._application_settings.app_launch = 1 171 self._application_settings.workspace_path = pathlib.Path(dialog_startup.global_var_startup_workspace) 172 173 constants.PYSSA_LOGGER.info("Demo projects are getting downloaded and extracted ...") 174 import zipfile 175 176 with zipfile.ZipFile(pathlib.Path(f"{constants.SETTINGS_DIR}/demo-projects.zip"), "r") as zip_ref: 177 zip_ref.extractall(pathlib.Path(f"{constants.SETTINGS_DIR}/demo-projects")) 178 constants.PYSSA_LOGGER.info( 179 "Demo projects are downloaded and extracted.\n Import of demo projects started ...", 180 ) 181 182 path_of_demo_projects = pathlib.Path(f"{constants.SETTINGS_DIR}/demo-projects") 183 tmp_project = project.Project("", dialog_startup.global_var_startup_workspace) 184 for tmp_filename in os.listdir(path_of_demo_projects): 185 try: 186 tmp_project = tmp_project.deserialize_project( 187 pathlib.Path(f"{path_of_demo_projects}/{tmp_filename}"), 188 self._application_settings, 189 ) 190 except exception.IllegalArgumentError: 191 constants.PYSSA_LOGGER.warning( 192 "The workspace path does not exist on this system, " "but this is due to the demo projects.", 193 ) 194 tmp_project.set_workspace_path(dialog_startup.global_var_startup_workspace) 195 new_filepath = pathlib.Path(f"{dialog_startup.global_var_startup_workspace}/{tmp_filename}") 196 tmp_project.serialize_project(new_filepath) 197 constants.PYSSA_LOGGER.info("Import process of demo projects finished.") 198 try: 199 os.remove(pathlib.Path(f"{constants.SETTINGS_DIR}/demo-projects.zip")) 200 except FileNotFoundError: 201 constants.PYSSA_LOGGER.warning("Zip archive of demo projects could not be found!") 202 constants.PYSSA_LOGGER.info("Serialize settings ...") 203 self._application_settings.serialize_settings() 204 constants.PYSSA_LOGGER.info("Serialize settings finished.") 205 206 QtWidgets.QApplication.restoreOverrideCursor() 207 208 globals.g_settings = main_window_util.setup_app_settings(self._application_settings) 209 self._application_settings = globals.g_settings 210 # </editor-fold> 211 # Check version number 212 main_window_util.check_version_number() 213 214 # <editor-fold desc="Class attributes"> 215 self._workspace_path = self._application_settings.workspace_path 216 self._workspace_status = f"Current workspace: {str(self._workspace_path)}" 217 self._workspace_label = QtWidgets.QLabel(f"Current Workspace: {self._workspace_path}") 218 self.prediction_configuration = prediction_configuration.PredictionConfiguration(True, "pdb70") 219 self.results_name = "" 220 self.no_of_selected_chains = 0 221 self.plot_dialog = QtWidgets.QDialog(self._view) 222 self.view_box = None 223 self.block_box_expert_install = basic_boxes.no_buttons( 224 "Local Colabfold installation", 225 "An installation process is currently running.", 226 QtWidgets.QMessageBox.Information, 227 ) 228 self.prediction_type = 0 229 self.current_session = current_session.CurrentSession("", "", "") 230 self.is_distance_plot_open = False 231 self.distance_plot_dialog = None 232 233 self.main_window_state = main_window_state.MainWindowState( 234 results_state.ResultsState(), 235 image_state.ImageState(), 236 ) 237 238 constants.PYSSA_LOGGER.info("Setup class attributes finished.") 239 # </editor-fold> 240 241 # sets up the status bar 242 self._setup_statusbar() 243 tools.create_directory(constants.SETTINGS_DIR, "scratch") 244 self._setup_default_configuration() 245 246 # if len(os.listdir(constants.LOG_PATH)) > 0: 247 # self.open_change_log() 248 249 constants.PYSSA_LOGGER.info("Setup rest of GUI related elements ...") 250 251 # <editor-fold desc="GUI page management"> 252 # -- Gui page management vars 253 self.batch_analysis_management: gui_page_management.GuiPageManagement 254 self.results_management: gui_page_management.GuiPageManagement 255 256 # management functions 257 self._create_batch_analysis_management() 258 self._create_results_management() 259 260 # </editor-fold> 261 262 # <editor-fold desc="Block box definitions"> 263 self.block_box_analysis = basic_boxes.no_buttons( 264 "Analysis", 265 "An analysis is currently running, please wait.", 266 QtWidgets.QMessageBox.Information, 267 ) 268 self.block_box_prediction: QtWidgets.QMessageBox = QtWidgets.QMessageBox() 269 self.block_box_images = basic_boxes.no_buttons( 270 "Analysis Images", 271 "Images getting created, please wait.", 272 QtWidgets.QMessageBox.Information, 273 ) 274 self.block_box_uni = basic_boxes.no_buttons("Generic", "Generic", QtWidgets.QMessageBox.Information) 275 276 # </editor-fold> 277 278 # configure gui element properties 279 self._view.ui.txt_results_aligned_residues.setAlignment(QtCore.Qt.AlignRight) 280 self._view.ui.table_pred_mono_prot_to_predict.setSizeAdjustPolicy( 281 QtWidgets.QAbstractScrollArea.AdjustToContents, 282 ) 283 self._view.ui.table_pred_mono_prot_to_predict.horizontalHeader().setDefaultAlignment(QtCore.Qt.AlignLeft) 284 self._view.ui.table_pred_multi_prot_to_predict.horizontalHeader().setDefaultAlignment(QtCore.Qt.AlignLeft) 285 self._view.ui.list_pred_analysis_multi_ref_chains.setSelectionMode( 286 QtWidgets.QAbstractItemView.ExtendedSelection, 287 ) 288 self._view.ui.list_pred_analysis_multi_model_chains.setSelectionMode( 289 QtWidgets.QAbstractItemView.ExtendedSelection, 290 ) 291 292 # helper attributes 293 self.pymol_session_specs = { 294 pyssa_keys.SESSION_SPEC_PROTEIN: [0, ""], 295 pyssa_keys.SESSION_SPEC_COLOR: [0, ""], 296 pyssa_keys.SESSION_SPEC_REPRESENTATION: [0, ""], 297 pyssa_keys.SESSION_SPEC_BG_COLOR: [0, ""], 298 } 299 300 # <editor-fold desc="Setup defaults for pages"> 301 self._init_fill_combo_boxes() 302 self._init_new_page() 303 self._init_use_page() 304 self._init_local_pred_mono_page() 305 self._init_local_pred_multi_page() 306 self._init_batch_analysis_page() 307 self._view.ui.action_toggle_notebook_visibility.setVisible(False) 308 self._view.ui.action_settings_model_w_off_colab_notebook.setVisible(False) 309 self.last_sidebar_button = QtWidgets.QPushButton() 310 self._view.ui.table_pred_mono_prot_to_predict.setEditTriggers( 311 self._view.ui.table_pred_mono_prot_to_predict.NoEditTriggers, 312 ) 313 self._view.ui.table_pred_multi_prot_to_predict.setEditTriggers( 314 self._view.ui.table_pred_multi_prot_to_predict.NoEditTriggers, 315 ) 316 self._view.ui.table_pred_analysis_mono_prot_to_predict.setEditTriggers( 317 self._view.ui.table_pred_analysis_mono_prot_to_predict.NoEditTriggers, 318 ) 319 self._view.ui.table_pred_analysis_multi_prot_to_predict.setEditTriggers( 320 self._view.ui.table_pred_analysis_multi_prot_to_predict.NoEditTriggers, 321 ) 322 323 # TODO: temp gui changes (need to be changed in the designer) 324 self._view.ui.lbl_hotspots_resi_show.setText("Residue(s) as sticks") 325 self._view.ui.lbl_hotspots_resi_hide.setText("Residue(s) as sticks") 326 327 # fixme: should the pdf documentation be accessible through the pyssa gui? 328 self._view.ui.action_help_docs_pdf.setText("Documentation") 329 self._view.ui.action_help_docs_pdf.setVisible(True) 330 self._view.ui.action_help_docs.setText("Tutorials") 331 self._view.ui.action_help_docs.setVisible(True) 332 333 if self._application_settings.wsl_install == 1 and self._application_settings.local_colabfold == 0: 334 self._view.ui.action_install_from_file.setVisible(True) 335 else: 336 self._view.ui.action_install_from_file.setVisible(False) 337 # </editor-fold> 338 339 self._connect_all_gui_elements() 340 341 self._project_watcher.show_valid_options(self._view.ui) 342 self._project_watcher.check_workspace_for_projects(self._workspace_path, self._view.ui) 343 344 self.threadpool = QtCore.QThreadPool() 345 # create scratch and cache dir 346 try: 347 filesystem_helpers.delete_directory(constants.SCRATCH_DIR) 348 except Exception as e: 349 constants.PYSSA_LOGGER.warning(f"Scratch path could not be deleted. {e}") 350 filesystem_helpers.create_directory(constants.SCRATCH_DIR) 351 filesystem_helpers.create_directory(constants.CACHE_DIR) 352 353 def start_worker_thread(self, worker_obj: object, post_process_func) -> None: # noqa: ANN001 354 """Sets up the worker, moves the worker to a thread and starts the thread. 355 356 Args: 357 worker_obj: an object of type <work>Worker (QObject). 358 post_process_func: a function which sould be executed if the worker is finished. 359 """ 360 self.tmp_thread = QtCore.QThread() 361 self.tmp_worker = worker_obj 362 self.tmp_thread = task_workers.setup_worker_for_work(self.tmp_thread, self.tmp_worker, post_process_func) 363 self.tmp_thread.start() 364 365 def _setup_statusbar(self) -> None: 366 """Sets up the status bar and fills it with the current workspace.""" 367 self._view.setStatusBar(self._view.status_bar) 368 self._view.status_bar.showMessage(str(self._workspace_label.text())) 369 370 def _setup_default_configuration(self) -> None: 371 """Sets up the default values for specific gui elements.""" 372 self._view.ui.lbl_current_project_name.setText("") 373 # menu 374 # side menu 375 376 # new project page 377 self._view.ui.btn_new_create_project.setEnabled(False) 378 self._view.ui.cb_new_add_reference.setCheckable(False) 379 self._view.ui.cb_new_add_reference.setStyleSheet("color: #E1E1E1;") 380 # open project page 381 self._view.ui.lbl_open_status_search.setText("") 382 self._view.ui.btn_open_open_project.setEnabled(False) 383 # delete project page 384 self._view.ui.lbl_delete_status_search.setText("") 385 self._view.ui.btn_delete_delete_project.setEnabled(False) 386 # edit project page 387 388 # view project page 389 390 # use project page 391 392 # new sequence page 393 # sequence vs .pdb page 394 self._view.ui.btn_s_v_p_start.setEnabled(False) 395 self._view.ui.list_s_v_p_ref_chains.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection) 396 # single analysis page 397 self._view.ui.lbl_analysis_model_chains.hide() 398 self._view.ui.list_analysis_model_chains.hide() 399 self._view.ui.btn_analysis_back.hide() 400 self._view.ui.btn_analysis_start.hide() 401 # batch analysis page 402 403 # results page 404 405 # image page 406 407 def _connect_all_gui_elements(self) -> None: 408 """Connects all gui elements with their corresponding slots.""" 409 self._view.ui.btn_info.clicked.connect(self.open_page_information) 410 411 # <editor-fold desc="Menu"> 412 self._view.ui.action_file_quit.triggered.connect(self.quit_app) 413 self._view.ui.action_file_restore_settings.triggered.connect(self.restore_settings) 414 self._view.ui.action_settings_edit_all.triggered.connect(self.open_settings_global) 415 self._view.ui.action_help_docs.triggered.connect(self.open_tutorial) 416 self._view.ui.action_help_docs_pdf.triggered.connect(self.open_documentation) 417 self._view.ui.action_help_about.triggered.connect(self.open_about) 418 self._view.ui.action_settings_open_logs.triggered.connect(self.open_logs) 419 self._view.ui.action_settings_clear_logs.triggered.connect(self.clear_all_log_files) 420 self._view.ui.action_help_changelog.triggered.connect(self.open_release_notes_in_standard_application) 421 # </editor-fold> 422 423 # <editor-fold desc="Side Menu"> 424 self._view.ui.btn_new_page.clicked.connect(self.display_new_page) 425 self._view.ui.btn_open_page.clicked.connect(self.display_open_page) 426 self._view.ui.btn_delete_page.clicked.connect(self.display_delete_page) 427 self._view.ui.btn_save_project.clicked.connect(self.save_project) 428 self._view.ui.btn_edit_page.clicked.connect(self.display_edit_page) 429 self._view.ui.btn_view_page.clicked.connect(self.display_view_page) 430 self._view.ui.btn_use_page.clicked.connect(self.display_use_page) 431 self._view.ui.btn_import_project.clicked.connect(self.import_project) 432 self._view.ui.btn_export_project.clicked.connect(self.export_current_project) 433 self._view.ui.btn_close_project.clicked.connect(self.close_project) 434 self._view.ui.btn_pred_cloud_monomer_page.clicked.connect(self.display_esm_pred_mono) 435 self._view.ui.btn_pred_local_monomer_page.clicked.connect(self.display_local_pred_mono) 436 self._view.ui.btn_pred_local_multimer_page.clicked.connect(self.display_local_pred_multi) 437 self._view.ui.btn_prediction_abort.clicked.connect(self.abort_prediction) 438 self._view.ui.btn_pred_analysis_monomer_page.clicked.connect(self.display_monomer_pred_analysis) 439 self._view.ui.btn_pred_analysis_multimer_page.clicked.connect(self.display_multimer_pred_analysis) 440 self._view.ui.btn_batch_analysis_page.clicked.connect(self.display_job_analysis_page) 441 self._view.ui.btn_image_analysis_page.clicked.connect(self.display_image_analysis_page) 442 self._view.ui.btn_results_page.clicked.connect(self.display_results_page) 443 # self._view.ui.btn_analysis_abort.clicked.connect(self.abort_analysis) 444 self._view.ui.btn_manage_session.clicked.connect(self.display_manage_pymol_session) 445 self._view.ui.btn_image_page.clicked.connect(self.display_image_page) 446 self._view.ui.btn_hotspots_page.clicked.connect(self.display_hotspots_page) 447 448 # </editor-fold> 449 450 # <editor-fold desc="New project page"> 451 self._view.ui.btn_new_choose_reference.clicked.connect(self.load_reference_in_project) 452 self._view.ui.txt_new_project_name.textChanged.connect(self.validate_project_name) 453 self._view.ui.txt_new_choose_reference.textChanged.connect(self.validate_reference_in_project) 454 self._view.ui.cb_new_add_reference.stateChanged.connect(self.show_add_reference) 455 self._view.ui.btn_new_create_project.clicked.connect(self.create_new_project) 456 457 # </editor-fold> 458 459 # <editor-fold desc="Open project page"> 460 self._view.ui.btn_open_open_project.clicked.connect(self.open_project) 461 self._view.ui.list_open_projects.doubleClicked.connect(self.open_project) 462 self._view.ui.txt_open_search.textChanged.connect(self.validate_open_search) 463 self._view.ui.txt_open_selected_project.textChanged.connect(self.activate_open_button) 464 self._view.ui.list_open_projects.currentItemChanged.connect(self.select_project_from_open_list) 465 466 # </editor-fold> 467 468 # <editor-fold desc="Delete project page"> 469 self._view.ui.btn_delete_delete_project.clicked.connect(self.delete_project) 470 self._view.ui.txt_delete_search.textChanged.connect(self.validate_delete_search) 471 self._view.ui.txt_delete_selected_projects.textChanged.connect(self.activate_delete_button) 472 self._view.ui.list_delete_projects.currentItemChanged.connect(self.select_project_from_delete_list) 473 474 # </editor-fold> 475 476 # <editor-fold desc="Edit project page"> 477 self._view.ui.btn_edit_page.clicked.connect(self.display_edit_page) 478 self._view.ui.list_edit_project_proteins.currentItemChanged.connect(self.check_for_cleaning) 479 self._view.ui.btn_edit_clean_new_prot.clicked.connect(self.clean_protein_new) 480 self._view.ui.btn_edit_clean_update_prot.clicked.connect(self.clean_protein_update) 481 self._view.ui.btn_edit_project_delete.clicked.connect(self.delete_protein) 482 self._view.ui.btn_edit_existing_protein_struct.clicked.connect(self.add_existing_protein) 483 self._view.ui.btn_edit_project_save.clicked.connect(self.save_selected_protein_structure_as_pdb_file) 484 self._view.ui.btn_edit_protein_rename.clicked.connect(self.rename_selected_protein_structure) 485 # </editor-fold> 486 487 # <editor-fold desc="View project page"> 488 self._view.ui.btn_view_project_show.clicked.connect(self.view_sequence) 489 self._view.ui.btn_view_project_show_structure.clicked.connect(self.view_structure) 490 self._view.ui.list_view_project_proteins.doubleClicked.connect(self.view_sequence) 491 self._view.ui.list_view_project_proteins.itemClicked.connect(self.view_show_options) 492 # </editor-fold> 493 494 # <editor-fold desc="Use project page"> 495 self._view.ui.txt_use_project_name.textChanged.connect(self.validate_use_project_name) 496 self._view.ui.btn_use_next.clicked.connect(self.show_protein_selection_for_use) 497 self._view.ui.txt_use_search.textChanged.connect(self.validate_use_search) 498 self._view.ui.btn_use_add_available_protein_structures.clicked.connect( 499 self.add_protein_structure_to_new_project, 500 ) 501 self._view.ui.list_use_available_protein_structures.doubleClicked.connect( 502 self.add_protein_structure_to_new_project, 503 ) 504 self._view.ui.list_use_available_protein_structures.itemClicked.connect(self.use_enable_add) 505 self._view.ui.btn_use_remove_selected_protein_structures.clicked.connect( 506 self.remove_protein_structure_to_new_project, 507 ) 508 self._view.ui.list_use_selected_protein_structures.doubleClicked.connect( 509 self.remove_protein_structure_to_new_project, 510 ) 511 self._view.ui.list_use_selected_protein_structures.itemClicked.connect(self.use_enable_remove) 512 self._view.ui.btn_use_back.clicked.connect(self.hide_protein_selection_for_use) 513 self._view.ui.btn_use_create_new_project.clicked.connect(self.pre_create_use_project) 514 515 # </editor-fold> 516 517 # <editor-fold desc="ESMFold Monomer Prediction page"> 518 self._view.ui.btn_esm_seq_to_predict.clicked.connect(self.cloud_esm_add_seq_to_predict) 519 self._view.ui.btn_esm_seq_to_predict_remove.clicked.connect(self.cloud_esm_remove) 520 self._view.ui.btn_esm_next.clicked.connect(self.cloud_esm_next) 521 self._view.ui.btn_esm_back.clicked.connect(self.cloud_esm_back) 522 self._view.ui.btn_esm_next_2.clicked.connect(self.cloud_esm_add_protein) 523 self._view.ui.btn_esm_back_2.clicked.connect(self.cloud_esm_back_2) 524 self._view.ui.txt_esm_prot_name.textChanged.connect(self.cloud_esm_validate_protein_name) 525 self._view.ui.txt_esm_prot_seq.textChanged.connect(self.cloud_esm_validate_protein_sequence) 526 self._view.ui.btn_esm_predict.clicked.connect(self.predict_esm_monomer) 527 528 self._view.ui.table_esm_prot_to_predict.itemSelectionChanged.connect(self.cloud_esm_item_changed) 529 # </editor-fold> 530 531 # <editor-fold desc="Monomer local prediction page"> 532 self._view.ui.btn_pred_mono_seq_to_predict.clicked.connect(self.local_pred_mono_add_seq_to_predict) 533 self._view.ui.btn_pred_mono_seq_to_predict_remove.clicked.connect(self.local_pred_mono_remove) 534 self._view.ui.btn_pred_mono_next.clicked.connect(self.local_pred_mono_next) 535 self._view.ui.btn_pred_mono_back.clicked.connect(self.local_pred_mono_back) 536 self._view.ui.btn_pred_mono_add_protein.clicked.connect(self.local_pred_mono_add_protein) 537 self._view.ui.btn_pred_mono_back_2.clicked.connect(self.local_pred_mono_back_2) 538 self._view.ui.txt_pred_mono_prot_name.textChanged.connect(self.local_pred_mono_validate_protein_name) 539 self._view.ui.txt_pred_mono_seq_name.textChanged.connect(self.local_pred_mono_validate_protein_sequence) 540 self._view.ui.btn_pred_mono_advanced_config.clicked.connect(self.show_prediction_configuration) 541 self._view.ui.btn_pred_mono_predict.clicked.connect(self.predict_local_monomer) 542 543 self._view.ui.table_pred_mono_prot_to_predict.itemSelectionChanged.connect(self.local_pred_mono_item_changed) 544 # </editor-fold> 545 546 # <editor-fold desc="Multimer prediction page"> 547 self._view.ui.btn_pred_multi_prot_to_predict_add.clicked.connect(self.local_pred_multi_add) 548 self._view.ui.btn_pred_multi_prot_to_predict_remove.clicked.connect(self.local_pred_multi_remove) 549 self._view.ui.btn_pred_multi_next.clicked.connect(self.local_pred_multi_next) 550 self._view.ui.btn_pred_multi_back.clicked.connect(self.local_pred_multi_back) 551 self._view.ui.btn_pred_multi_prot_to_predict_add_2.clicked.connect(self.local_pred_multi_prot_to_predict_add_2) 552 self._view.ui.btn_pred_multi_back_2.clicked.connect(self.local_pred_multi_back_2) 553 self._view.ui.txt_pred_multi_prot_name.textChanged.connect(self.local_pred_multi_validate_protein_name) 554 self._view.ui.txt_pred_multi_prot_seq.textChanged.connect(self.local_pred_multi_validate_protein_sequence) 555 self._view.ui.btn_pred_multi_prot_seq_add.clicked.connect(self.local_pred_multi_add_sequence_to_list) 556 self._view.ui.btn_pred_multi_prot_seq_overview_remove.clicked.connect( 557 self.local_pred_multi_remove_sequence_to_list, 558 ) 559 self._view.ui.btn_pred_multi_advanced_config.clicked.connect(self.show_prediction_configuration) 560 self._view.ui.btn_pred_multi_predict.clicked.connect(self.predict_local_multimer) 561 562 self._view.ui.list_pred_multi_prot_seq_overview.itemClicked.connect( 563 self.local_pred_multi_prot_seq_overview_item_changed, 564 ) 565 self._view.ui.table_pred_multi_prot_to_predict.itemSelectionChanged.connect( 566 self.local_pred_multi_prot_to_predict_item_changed, 567 ) 568 # </editor-fold> 569 570 # <editor-fold desc="Monomer Prediction + Analysis page"> 571 # <editor-fold desc="Prediction section"> 572 self._view.ui.btn_pred_analysis_mono_seq_to_predict.clicked.connect(self.mono_pred_analysis_add_seq_to_predict) 573 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.clicked.connect( 574 self.mono_pred_analysis_remove_protein_to_predict, 575 ) 576 self._view.ui.btn_pred_analysis_mono_next.clicked.connect(self.mono_pred_analysis_next) 577 self._view.ui.btn_pred_analysis_mono_back.clicked.connect(self.mono_pred_analysis_back) 578 self._view.ui.btn_pred_analysis_mono_add_protein.clicked.connect(self.mono_pred_analysis_add_protein) 579 self._view.ui.btn_pred_analysis_mono_back_2.clicked.connect(self.mono_pred_analysis_back_2) 580 self._view.ui.txt_pred_analysis_mono_prot_name.textChanged.connect( 581 self.mono_pred_analysis_validate_protein_name, 582 ) 583 self._view.ui.txt_pred_analysis_mono_seq_name.textChanged.connect( 584 self.mono_pred_analysis_validate_protein_sequence, 585 ) 586 self._view.ui.btn_pred_mono_advanced_config_2.clicked.connect(self.show_prediction_configuration) 587 self._view.ui.btn_pred_analysis_mono_go_analysis_setup.clicked.connect(self.switch_monomer_pred_analysis_tab) 588 self._view.ui.table_pred_analysis_mono_prot_to_predict.itemSelectionChanged.connect( 589 self.mono_pred_analysis_prediction_overview_item_clicked, 590 ) 591 592 # </editor-fold> 593 594 # <editor-fold desc="Analysis section"> 595 self._view.ui.btn_pred_analysis_mono_add.clicked.connect(self.mono_pred_analysis_structure_analysis_add) 596 self._view.ui.btn_pred_analysis_mono_remove.clicked.connect(self.remove_mono_pred_analysis_analysis_run) 597 self._view.ui.btn_pred_analysis_mono_back_3.clicked.connect(self.mono_pred_analysis_structure_analysis_back_3) 598 self._view.ui.btn_pred_analysis_mono_next_2.clicked.connect(self.mono_pred_analysis_structure_analysis_next_2) 599 self._view.ui.btn_pred_analysis_mono_back_4.clicked.connect(self.mono_pred_analysis_structure_analysis_back_4) 600 self._view.ui.btn_pred_analysis_mono_next_3.clicked.connect(self.mono_pred_analysis_structure_analysis_next_3) 601 self._view.ui.btn_pred_analysis_mono_back_5.clicked.connect(self.mono_pred_analysis_structure_analysis_back_5) 602 self._view.ui.btn_pred_analysis_mono_next_4.clicked.connect(self.mono_pred_analysis_structure_analysis_next_4) 603 self._view.ui.box_pred_analysis_mono_prot_struct_1.currentIndexChanged.connect( 604 self.check_mono_pred_analysis_if_prot_structs_are_filled, 605 ) 606 self._view.ui.box_pred_analysis_mono_prot_struct_2.currentIndexChanged.connect( 607 self.check_mono_pred_analysis_if_prot_structs_are_filled, 608 ) 609 self._view.ui.list_pred_analysis_mono_ref_chains.itemSelectionChanged.connect( 610 self.count_mono_pred_analysis_selected_chains_for_prot_struct_1, 611 ) 612 self._view.ui.list_pred_analysis_mono_model_chains.itemSelectionChanged.connect( 613 self.check_mono_pred_analysis_if_same_no_of_chains_selected, 614 ) 615 self._view.ui.btn_pred_analysis_mono_back_pred_setup.clicked.connect(self.switch_monomer_pred_analysis_tab) 616 self._view.ui.btn_pred_analysis_mono_start.clicked.connect(self.start_monomer_prediction_analysis) 617 self._view.ui.list_pred_analysis_mono_overview.clicked.connect( 618 self.mono_pred_analysis_structure_analysis_overview_clicked, 619 ) 620 621 # </editor-fold> 622 623 # </editor-fold> 624 625 # <editor-fold desc="Multimer Prediction + Analysis page"> 626 # <editor-fold desc="Prediction section"> 627 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add.clicked.connect(self.multi_pred_analysis_add) 628 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove.clicked.connect( 629 self.multi_pred_analysis_remove_protein_to_predict, 630 ) 631 self._view.ui.btn_pred_analysis_multi_next.clicked.connect(self.multi_pred_analysis_next) 632 self._view.ui.btn_pred_analysis_multi_back.clicked.connect(self.multi_pred_analysis_back) 633 self._view.ui.btn_pred_analysis_multi_prot_seq_add.clicked.connect( 634 self.multi_pred_analysis_add_sequence_to_list, 635 ) 636 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove.clicked.connect( 637 self.multi_pred_analysis_remove_sequence_to_list, 638 ) 639 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2.clicked.connect( 640 self.multi_pred_analysis_add_protein_to_predict, 641 ) 642 self._view.ui.btn_pred_analysis_multi_back_2.clicked.connect(self.multi_pred_analysis_back_2) 643 644 self._view.ui.txt_pred_analysis_multi_prot_name.textChanged.connect( 645 self.multi_pred_analysis_validate_protein_name, 646 ) 647 self._view.ui.txt_pred_analysis_multi_prot_seq.textChanged.connect( 648 self.multi_pred_analysis_validate_protein_sequence, 649 ) 650 self._view.ui.btn_pred_analysis_multi_advanced_config.clicked.connect(self.show_prediction_configuration) 651 self._view.ui.btn_pred_analysis_multi_go_analysis_setup.clicked.connect(self.switch_multimer_pred_analysis_tab) 652 653 self._view.ui.list_pred_analysis_multi_prot_seq_overview.clicked.connect( 654 self.multi_pred_analysis_prot_seq_overview_item_changed, 655 ) 656 self._view.ui.table_pred_analysis_multi_prot_to_predict.itemSelectionChanged.connect( 657 self.multi_pred_analysis_prot_to_predict_item_changed, 658 ) 659 660 # </editor-fold> 661 662 # <editor-fold desc="Analysis section"> 663 self._view.ui.btn_pred_analysis_multi_add.clicked.connect(self.multi_pred_analysis_structure_analysis_add) 664 self._view.ui.btn_pred_analysis_multi_remove.clicked.connect(self.remove_multi_pred_analysis_analysis_run) 665 self._view.ui.btn_pred_analysis_multi_back_3.clicked.connect(self.multi_pred_analysis_structure_analysis_back_3) 666 self._view.ui.btn_pred_analysis_multi_next_2.clicked.connect(self.multi_pred_analysis_structure_analysis_next_2) 667 self._view.ui.btn_pred_analysis_multi_back_4.clicked.connect(self.multi_pred_analysis_structure_analysis_back_4) 668 self._view.ui.btn_pred_analysis_multi_next_3.clicked.connect(self.multi_pred_analysis_structure_analysis_next_3) 669 self._view.ui.btn_pred_analysis_multi_back_5.clicked.connect(self.multi_pred_analysis_structure_analysis_back_5) 670 self._view.ui.btn_pred_analysis_multi_next_4.clicked.connect(self.multi_pred_analysis_structure_analysis_next_4) 671 self._view.ui.box_pred_analysis_multi_prot_struct_1.currentIndexChanged.connect( 672 self.check_multi_pred_analysis_if_prot_structs_are_filled, 673 ) 674 self._view.ui.box_pred_analysis_multi_prot_struct_2.currentIndexChanged.connect( 675 self.check_multi_pred_analysis_if_prot_structs_are_filled, 676 ) 677 self._view.ui.list_pred_analysis_multi_ref_chains.itemSelectionChanged.connect( 678 self.count_multi_pred_analysis_selected_chains_for_prot_struct_1, 679 ) 680 self._view.ui.list_pred_analysis_multi_model_chains.itemSelectionChanged.connect( 681 self.check_multi_pred_analysis_if_same_no_of_chains_selected, 682 ) 683 self._view.ui.btn_pred_analysis_multi_back_pred_setup.clicked.connect(self.switch_multimer_pred_analysis_tab) 684 self._view.ui.btn_pred_analysis_multi_start.clicked.connect(self.start_multimer_prediction_analysis) 685 self._view.ui.list_pred_analysis_multi_overview.clicked.connect( 686 self.multi_pred_analysis_structure_analysis_overview_clicked, 687 ) 688 # </editor-fold> 689 690 # </editor-fold> 691 692 # <editor-fold desc="Structure analysis page"> 693 self._view.ui.btn_analysis_batch_add.clicked.connect(self.structure_analysis_add) 694 self._view.ui.btn_analysis_batch_remove.clicked.connect(self.remove_analysis_run) 695 self._view.ui.btn_analysis_batch_back.clicked.connect(self.structure_analysis_back) 696 self._view.ui.btn_analysis_batch_next.clicked.connect(self.structure_analysis_next) 697 self._view.ui.btn_analysis_batch_back_2.clicked.connect(self.structure_analysis_back_2) 698 self._view.ui.btn_analysis_batch_next_2.clicked.connect(self.structure_analysis_next_2) 699 self._view.ui.btn_analysis_batch_back_3.clicked.connect(self.structure_analysis_back_3) 700 self._view.ui.btn_analysis_batch_next_3.clicked.connect(self.structure_analysis_next_3) 701 self._view.ui.box_analysis_batch_prot_struct_1.currentIndexChanged.connect( 702 self.check_if_prot_structs_are_filled_batch, 703 ) 704 self._view.ui.box_analysis_batch_prot_struct_2.currentIndexChanged.connect( 705 self.check_if_prot_structs_are_filled_batch, 706 ) 707 self._view.ui.list_analysis_batch_ref_chains.itemSelectionChanged.connect( 708 self.count_batch_selected_chains_for_prot_struct_1, 709 ) 710 self._view.ui.list_analysis_batch_model_chains.itemSelectionChanged.connect( 711 self.check_if_same_no_of_chains_selected_batch, 712 ) 713 self._view.ui.btn_analysis_batch_start.clicked.connect(self.start_process_batch) 714 self._view.ui.list_analysis_batch_overview.clicked.connect(self.structure_analysis_overview_clicked) 715 716 # </editor-fold> 717 718 # <editor-fold desc="Analysis images page"> 719 self._view.ui.btn_add_analysis_images_struct_analysis.clicked.connect( 720 self.add_protein_pair_to_image_creation_queue, 721 ) 722 self._view.ui.list_analysis_images_struct_analysis.doubleClicked.connect( 723 self.add_protein_pair_to_image_creation_queue, 724 ) 725 self._view.ui.list_analysis_images_struct_analysis.clicked.connect(self.analysis_images_enable_add) 726 self._view.ui.btn_remove_analysis_images_creation_struct_analysis.clicked.connect( 727 self.remove_protein_pair_from_image_creation_queue, 728 ) 729 self._view.ui.list_analysis_images_creation_struct_analysis.doubleClicked.connect( 730 self.remove_protein_pair_from_image_creation_queue, 731 ) 732 self._view.ui.list_analysis_images_creation_struct_analysis.clicked.connect(self.analysis_images_enable_remove) 733 self._view.ui.btn_start_automatic_image_creation.clicked.connect(self.start_automatic_image_creation) 734 735 # </editor-fold> 736 737 # <editor-fold desc="Results page"> 738 self._view.ui.cb_results_analysis_options.currentIndexChanged.connect(self.load_results) 739 self._view.ui.btn_color_rmsd.clicked.connect(self.color_protein_pair_by_rmsd) 740 self._view.ui.btn_view_struct_alignment.clicked.connect(self.display_structure_alignment) 741 self._view.ui.btn_view_distance_plot.clicked.connect(self.display_distance_plot) 742 self._view.ui.btn_view_distance_histogram.clicked.connect(self.display_distance_histogram) 743 self._view.ui.btn_view_interesting_region.clicked.connect(self.display_interesting_region) 744 self._view.ui.btn_view_distance_table.clicked.connect(self.display_distance_table) 745 746 # </editor-fold> 747 748 # <editor-fold desc="Manage"> 749 self._view.ui.box_manage_choose_protein.activated.connect(self.choose_manage_open_protein) 750 self._view.ui.box_manage_choose_color.activated.connect(self.choose_manage_color_selected_protein) 751 self._view.ui.box_manage_choose_representation.activated.connect(self.choose_manage_representation) 752 self._view.ui.box_manage_choose_bg_color.activated.connect(self.choose_manage_bg_color) 753 self._view.ui.btn_disulfid_bond_show.clicked.connect(self.show_disulfid_bonds_as_sticks) 754 self._view.ui.btn_disulfid_bond_hide.clicked.connect(self.hide_disulfid_bonds_as_sticks) 755 756 # </editor-fold> 757 758 # <editor-fold desc="Image page"> 759 self._view.ui.btn_update_scene.clicked.connect(self.update_scene) 760 self._view.ui.btn_save_scene.clicked.connect(self.save_scene) 761 self._view.ui.btn_save_image.clicked.connect(self.save_image) 762 self._view.ui.btn_preview_image.clicked.connect(self.preview_image) 763 self._view.ui.box_representation.activated.connect(self.show_representation) 764 self._view.ui.box_bg_color.activated.connect(self.choose_bg_color) 765 self._view.ui.box_renderer.activated.connect(self.choose_renderer) 766 self._view.ui.box_ray_trace_mode.activated.connect(self.choose_ray_trace_mode) 767 self._view.ui.box_ray_texture.activated.connect(self.choose_ray_texture) 768 self._view.ui.cb_transparent_bg.stateChanged.connect(self.decide_transparent_bg) 769 self._view.ui.cb_ray_tracing.stateChanged.connect(self.decide_ray_tracing) 770 771 # </editor-fold> 772 773 # <editor-fold desc="Hotspots page"> 774 self._view.ui.list_hotspots_choose_protein.currentItemChanged.connect(self.open_protein_for_hotspots) 775 self._view.ui.btn_hotspots_resi_show.clicked.connect(self.show_resi_sticks) 776 self._view.ui.btn_hotspots_resi_hide.clicked.connect(self.hide_resi_sticks) 777 self._view.ui.btn_hotspots_resi_zoom.clicked.connect(self.zoom_resi_position) 778 779 # </editor-fold> 780 781 def restore_settings(self) -> None: 782 """Restores the settings.xml file to the default values.""" 783 out = gui_utils.warning_dialog_restore_settings("Are you sure you want to restore all settings?") 784 if out: 785 tools.restore_default_settings(self._application_settings) 786 self._view.status_bar.showMessage("Settings were successfully restored.") 787 logging.info("Settings were successfully restored.") 788 else: 789 self._view.status_bar.showMessage("Settings were not modified.") 790 logging.info("Settings were not modified.") 791 792 def quit_app(self) -> None: 793 """Closes the entire plugin.""" 794 self._view.quit_app() 795 796 @staticmethod 797 def clear_all_log_files() -> None: 798 """Clears all log files generated under .pyssa/logs.""" 799 response = basic_boxes.yes_or_no( 800 "Clear log files", 801 "Are you sure you want to delete all log files?", 802 QtWidgets.QMessageBox.Information, 803 ) 804 if response: 805 try: 806 shutil.rmtree(str(constants.LOG_PATH)) 807 except PermissionError: 808 print("The active log file was not deleted.") 809 if len(os.listdir(str(constants.LOG_PATH))) == 1: 810 basic_boxes.ok("Clear log files", "All log files could be deleted.", QtWidgets.QMessageBox.Information) 811 constants.PYSSA_LOGGER.info("All log files were deleted.") 812 else: 813 basic_boxes.ok("Clear log files", "Not all log files could be deleted.", QtWidgets.QMessageBox.Warning) 814 constants.PYSSA_LOGGER.warning("Not all log files were deleted!") 815 816 # <editor-fold desc="Open extra views"> 817 def open_settings_global(self) -> None: 818 """Opens the dialog for the global settings.""" 819 dialog = dialog_settings_global.DialogSettingsGlobal() 820 dialog.exec_() 821 self._application_settings = self._application_settings.deserialize_settings() 822 globals.g_settings = self._application_settings 823 self._workspace_path = globals.g_settings.workspace_path 824 self._workspace_label = QtWidgets.QLabel(f"Current Workspace: {self._workspace_path}") 825 self._setup_statusbar() 826 827 def open_logs(self) -> None: 828 """Opens a file explorer with all log files and can open a log file in the default application.""" 829 file_dialog = QtWidgets.QFileDialog() 830 log_path = str(constants.LOG_PATH) 831 file_dialog.setDirectory(log_path) 832 file_path, _ = file_dialog.getOpenFileName(self._view, "Select a log file to open", "", "LOG File (*.log)") 833 if file_path: 834 os.startfile(file_path) 835 836 @staticmethod 837 def open_tutorial() -> None: 838 """Opens the official tutorial pdf file.""" 839 tmp_dialog = dialog_tutorial_videos.TutorialVideosDialog() 840 tmp_dialog.exec_() 841 842 @staticmethod 843 def open_documentation() -> None: 844 """Opens the official plugin documentation as PDF.""" 845 os.startfile(constants.DOCS_PATH) 846 847 @staticmethod 848 def open_about() -> None: 849 """Opens the About dialog.""" 850 dialog = dialog_about.DialogAbout() 851 dialog.exec_() 852 853 def open_page_information(self) -> None: 854 """Opens the message box, to display extra information based on the page.""" 855 with open( 856 f"{constants.PAGE_HELP_PATHS_DICT[self._view.ui.lbl_page_title.text()]}", 857 "r", 858 encoding="utf-8", 859 ) as file: 860 html_content = file.read() 861 file.close() 862 tmp_dialog = dialog_help.DialogHelp(html_content) 863 tmp_dialog.exec_() 864 865 @staticmethod 866 def open_release_notes_in_standard_application() -> None: 867 """Opens the release notes in the default app.""" 868 os.startfile(constants.CHANGELOG_HTML_PATH) 869 870 # </editor-fold> 871 872 # def open_change_log(self) -> None: 873 # """Opens change log based on the last run pyssa version. 874 # 875 # Notes: 876 # Change log opens only if the last pyssa version is older than the current one. 877 # """ 878 # last_version = f"v{self.get_version_from_latest_log_file(self.get_filepath_of_latest_log_file())}" 879 # if last_version != constants.VERSION_NUMBER: 880 # self.open_release_notes_in_standard_application() 881 # 882 # def get_version_from_latest_log_file(self, a_filepath: pathlib.Path) -> str: 883 # """Gets the pyssa version of the latest log file. 884 # 885 # Args: 886 # a_filepath: the filepath to the latest log file. 887 # """ 888 # with open(str(a_filepath), "r", encoding="utf-8") as file: 889 # file_content = file.read() 890 # file.close() 891 # # Define the regex pattern to extract the version number 892 # pattern = r"PySSA started with version v(\d+\.\d+\.\d+)" 893 # # Search for the pattern in the text 894 # match = re.search(pattern, file_content) 895 # # Check if a match is found 896 # if match: 897 # version_number = match.group(1) 898 # print("Extracted version number:", version_number) 899 # else: 900 # print("Version number not found in the text.") 901 # version_number = None 902 # return version_number 903 # 904 # def get_filepath_of_latest_log_file(self) -> pathlib.Path: 905 # """Gets the filepath of the latest log file. 906 # 907 # Raises: 908 # FileNotFoundError: If no log files can be found in the log directory. 909 # """ 910 # # Get a list of files in the directory 911 # files = [f for f in os.listdir(constants.LOG_PATH) if os.path.isfile(os.path.join(constants.LOG_PATH, f))] 912 # # Filter files to include only log files (adjust the extension accordingly) 913 # log_files = [f for f in files if f.endswith(".log")] 914 # # Check if there are any log files 915 # if not log_files: 916 # raise FileNotFoundError("No log files found in the directory.") 917 # # Get the full path of each log file 918 # log_files_paths = [os.path.join(constants.LOG_PATH, f) for f in log_files] 919 # # Get the latest log file based on modification time 920 # latest_log_file_index = log_files_paths.index(max(log_files_paths, key=os.path.getmtime)) - 1 921 # return pathlib.Path(log_files_paths[latest_log_file_index]) 922 923 # <editor-fold desc="Logic related methods"> 924 925 # <editor-fold desc="New project page functions"> 926 def create_new_project(self) -> None: 927 """Creates a new project with the content of the new page.""" 928 # <editor-fold desc="Checks"> 929 if self._application_settings.wsl_install == 0: 930 basic_boxes.ok( 931 "Create new project", 932 "Please install local colabfold to create a project!", 933 QtWidgets.QMessageBox.Warning, 934 ) 935 return 936 if self._application_settings.local_colabfold == 0: 937 basic_boxes.ok( 938 "Create new project", 939 "Please install local colabfold to create a project!", 940 QtWidgets.QMessageBox.Warning, 941 ) 942 return 943 944 # </editor-fold> 945 946 self._view.wait_spinner.start() 947 an_add_protein_flag: bool = False 948 if self._view.ui.cb_new_add_reference.checkState() == 2: 949 an_add_protein_flag = True 950 951 self._active_task = tasks.Task( 952 target=main_presenter_async.create_new_project, 953 args=( 954 self._view.ui.txt_new_project_name.text(), 955 self._workspace_path, 956 an_add_protein_flag, 957 self._view.ui.txt_new_choose_reference.text(), 958 ), 959 post_func=self.__await_create_new_project, 960 ) 961 self._active_task.start() 962 self.update_status("Creating new project ...") 963 964 def __await_create_new_project(self, a_result: tuple) -> None: 965 self._current_project: "project.Project" = a_result[1] 966 constants.PYSSA_LOGGER.info(f"Created the project {self._current_project.get_project_name()}.") 967 self._view.ui.cb_new_add_reference.setCheckState(0) 968 self._project_watcher.current_project = self._current_project 969 constants.PYSSA_LOGGER.info( 970 f"{self._project_watcher.current_project.get_project_name()} is the current project.", 971 ) 972 self._project_watcher.on_home_page = False 973 # update gui 974 self._project_watcher.show_valid_options(self._view.ui) 975 self._view.ui.lbl_current_project_name.setText(self._current_project.get_project_name()) 976 self.main_window_state = main_window_state.MainWindowState( 977 results_state.ResultsState(), 978 image_state.ImageState(), 979 ) 980 self.display_view_page() 981 self._view.wait_spinner.stop() 982 self.update_status(self._workspace_status) 983 984 # </editor-fold> 985 986 # <editor-fold desc="Open project page functions"> 987 def open_project(self) -> None: 988 """Initiates the task to open an existing project.""" 989 self._view.wait_spinner.start() 990 self._active_task = tasks.Task( 991 target=main_presenter_async.open_project, 992 args=( 993 self._workspace_path, 994 self._view.ui.txt_open_selected_project.text(), 995 self._application_settings, 996 ), 997 post_func=self.__await_open_project, 998 ) 999 self._active_task.start() 1000 self.update_status("Opening existing project ...") 1001 1002 def __await_open_project(self, a_result: tuple) -> None: 1003 self._current_project = a_result[1] 1004 self._project_watcher.current_project = self._current_project 1005 constants.PYSSA_LOGGER.info( 1006 f"{self._project_watcher.current_project.get_project_name()} is the current project.", 1007 ) 1008 self._view.ui.lbl_current_project_name.setText(self._current_project.get_project_name()) 1009 self._project_watcher.on_home_page = False 1010 self._project_watcher.show_valid_options(self._view.ui) 1011 cmd.reinitialize() 1012 self._view.ui.btn_manage_session.hide() 1013 self.display_view_page() 1014 self.main_window_state = main_window_state.MainWindowState( 1015 results_state.ResultsState(), 1016 image_state.ImageState(), 1017 ) 1018 self._view.wait_spinner.stop() 1019 self.update_status(self._workspace_status) 1020 1021 # </editor-fold> 1022 1023 # <editor-fold desc="Delete project page functions"> 1024 def delete_project(self) -> None: 1025 """Deletes an existing project.""" 1026 # popup message which warns the user that the selected project gets deleted 1027 response: bool = gui_utils.warning_message_project_gets_deleted() 1028 tmp_project_name = self._view.ui.txt_delete_selected_projects.text() 1029 if response is True: 1030 os.remove(pathlib.Path(f"{self._workspace_path}/{self._view.ui.txt_delete_selected_projects.text()}")) 1031 if self._view.ui.txt_delete_selected_projects.text() == self._view.ui.lbl_current_project_name.text(): 1032 self._view.ui.lbl_current_project_name.clear() 1033 self._view.ui.txt_delete_selected_projects.clear() 1034 # update list 1035 self._view.ui.list_delete_projects.clear() 1036 # pre-process 1037 self._view.status_bar.showMessage(self._workspace_label.text()) 1038 self._view.ui.list_delete_projects.clear() 1039 self._view.status_bar.showMessage(self._workspace_label.text()) 1040 tools.scan_workspace_for_valid_projects(self._workspace_path, self._view.ui.list_delete_projects) 1041 constants.PYSSA_LOGGER.info(f"The project {tmp_project_name} was successfully deleted.") 1042 if self._view.ui.list_delete_projects.count() == 0: 1043 self.display_home_page() 1044 self._project_watcher.check_workspace_for_projects(self._workspace_path, self._view.ui) 1045 else: 1046 constants.PYSSA_LOGGER.info("No project has been deleted. No changes were made.") 1047 1048 # </editor-fold> 1049 1050 # <editor-fold desc="Save project functions"> 1051 def save_project(self) -> None: 1052 """Saves the project.xml.""" 1053 self._view.wait_spinner.start() 1054 self.last_sidebar_button = styles.color_sidebar_buttons( 1055 self.last_sidebar_button, 1056 self._view.ui.btn_save_project, 1057 ) 1058 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 1059 self._active_task = tasks.Task( 1060 target=main_presenter_async.save_project, 1061 args=(self._current_project, 0), 1062 post_func=self.__await_save_project, 1063 ) 1064 self._active_task.start() 1065 self.update_status("Saving current project ...") 1066 1067 def __await_save_project(self, result: tuple) -> None: 1068 self._view.wait_spinner.stop() 1069 self.update_status(self._workspace_status) 1070 basic_boxes.ok("Save Project", "The project was successfully saved.", QtWidgets.QMessageBox.Information) 1071 1072 # </editor-fold> 1073 1074 # <editor-fold desc="Edit project page functions"> 1075 def check_for_cleaning(self) -> None: 1076 """Checks if the selected protein can be cleaned.""" 1077 self._view.wait_spinner.start() 1078 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 1079 try: 1080 tmp_protein_name: str = self._view.ui.list_edit_project_proteins.currentItem().text() 1081 except AttributeError: 1082 self._view.wait_spinner.stop() 1083 return 1084 self._active_task = tasks.Task( 1085 target=main_presenter_async.check_for_cleaning, 1086 args=( 1087 tmp_protein_name, 1088 self._current_project, 1089 ), 1090 post_func=self.__await_check_for_cleaning, 1091 ) 1092 self._active_task.start() 1093 self.update_status("Checking protein properties ...") 1094 1095 def __await_check_for_cleaning(self, result: tuple) -> None: 1096 # check if selected protein contains any organic or solvent molecules which can be removed 1097 tmp_is_cleanable: bool = result[1] 1098 tmp_is_in_protein_pair: bool = result[2] 1099 if tmp_is_cleanable: 1100 gui_elements_to_show = [ 1101 self._view.ui.lbl_edit_clean_new_prot, 1102 self._view.ui.btn_edit_clean_new_prot, 1103 self._view.ui.lbl_edit_clean_update_prot, 1104 self._view.ui.btn_edit_clean_update_prot, 1105 ] 1106 gui_utils.show_gui_elements(gui_elements_to_show) 1107 else: 1108 gui_elements_to_hide = [ 1109 self._view.ui.lbl_edit_clean_new_prot, 1110 self._view.ui.btn_edit_clean_new_prot, 1111 self._view.ui.lbl_edit_clean_update_prot, 1112 self._view.ui.btn_edit_clean_update_prot, 1113 ] 1114 gui_utils.hide_gui_elements(gui_elements_to_hide) 1115 # check if selected protein is in any existing protein pair 1116 if tmp_is_in_protein_pair: 1117 gui_elements_to_hide = [ 1118 self._view.ui.label_12, 1119 self._view.ui.btn_edit_project_delete, 1120 ] 1121 gui_utils.hide_gui_elements(gui_elements_to_hide) 1122 else: 1123 gui_elements_to_show = [ 1124 self._view.ui.label_12, 1125 self._view.ui.btn_edit_project_delete, 1126 ] 1127 gui_utils.show_gui_elements(gui_elements_to_show) 1128 self._view.ui.btn_edit_project_save.show() 1129 self._view.ui.label_13.show() 1130 self._view.ui.label_15.show() 1131 self._view.ui.btn_edit_protein_rename.show() 1132 self._view.ui.btn_manage_session.show() 1133 self._project_watcher.show_valid_options(self._view.ui) 1134 self._view.wait_spinner.stop() 1135 self.update_status(self._workspace_status) 1136 1137 def clean_protein_new(self) -> None: 1138 """Cleans the selected protein structure and creates a new cleaned structure.""" 1139 self._view.wait_spinner.start() 1140 self._active_task = tasks.Task( 1141 target=main_presenter_async.clean_protein_new, 1142 args=( 1143 self._view.ui.list_edit_project_proteins.currentItem().text().replace(".pdb", ""), 1144 self._current_project, 1145 ), 1146 post_func=self.__await_clean_protein_new, 1147 ) 1148 self._active_task.start() 1149 self.update_status("Duplicating and cleaning protein ...") 1150 1151 def __await_clean_protein_new(self, result: tuple) -> None: 1152 self._init_edit_page() 1153 self._project_watcher.show_valid_options(self._view.ui) 1154 self._view.wait_spinner.stop() 1155 self.update_status(self._workspace_status) 1156 1157 def clean_protein_update(self) -> None: 1158 """Cleans the selected protein structure.""" 1159 self._view.wait_spinner.start() 1160 if basic_boxes.yes_or_no( 1161 "Clean protein", 1162 "Are you sure you want to clean this protein?\n" "This will remove all organic and solvent components!", 1163 QtWidgets.QMessageBox.Information, 1164 ): 1165 self._active_task = tasks.Task( 1166 target=main_presenter_async.clean_protein_update, 1167 args=( 1168 self._view.ui.list_edit_project_proteins.currentItem().text().replace(".pdb", ""), 1169 self._current_project, 1170 ), 1171 post_func=self.__await_clean_protein_update, 1172 ) 1173 self._active_task.start() 1174 self.update_status("Cleaning protein ...") 1175 else: 1176 constants.PYSSA_LOGGER.info("No protein has been cleaned.") 1177 self._view.wait_spinner.stop() 1178 1179 def __await_clean_protein_update(self) -> None: 1180 self._init_edit_page() 1181 self._project_watcher.show_valid_options(self._view.ui) 1182 self._view.wait_spinner.stop() 1183 self.update_status(self._workspace_status) 1184 1185 def delete_protein(self) -> None: 1186 """Deletes the selected protein structure.""" 1187 self._view.wait_spinner.start() 1188 if gui_utils.warning_message_protein_gets_deleted(): 1189 self._active_task = tasks.Task( 1190 target=main_presenter_async.delete_protein, 1191 args=( 1192 self._view.ui.list_edit_project_proteins.currentItem().text(), 1193 self._current_project, 1194 ), 1195 post_func=self.__await_delete_protein, 1196 ) 1197 self._active_task.start() 1198 self.update_status("Deleting protein ...") 1199 else: 1200 constants.PYSSA_LOGGER.info("No protein was deleted.") 1201 self._view.wait_spinner.stop() 1202 1203 def __await_delete_protein(self) -> None: 1204 self._init_edit_page() 1205 self._project_watcher.show_valid_options(self._view.ui) 1206 self._view.wait_spinner.stop() 1207 self.update_status(self._workspace_status) 1208 1209 def add_existing_protein(self) -> None: 1210 """Opens a dialog to adds an existing protein structure to the project.""" 1211 self.tmp_dialog = view_add_protein.AddProteinView() 1212 self.tmp_dialog.return_value.connect(self.post_add_existing_protein) 1213 self.tmp_dialog.show() 1214 1215 def post_add_existing_protein(self, return_value: tuple) -> None: 1216 """Adds an existing protein structure to the current project either by id or from the filesystem. 1217 1218 Args: 1219 return_value: a tuple consisting of the filepath or PDB id and the length of the first one. 1220 """ 1221 self._view.wait_spinner.start() 1222 if return_value[1] > 0: 1223 self._active_task = tasks.Task( 1224 target=main_presenter_async.add_existing_protein_to_project, 1225 args=(return_value, self._current_project), 1226 post_func=self.__await_post_add_existing_protein, 1227 ) 1228 self._active_task.start() 1229 self.update_status("Adding protein to current project ...") 1230 else: 1231 self._view.wait_spinner.stop() 1232 self.display_edit_page() 1233 1234 def __await_post_add_existing_protein(self, result: tuple) -> None: 1235 self._current_project = result[1] 1236 self._project_watcher.show_valid_options(self._view.ui) 1237 self._view.wait_spinner.stop() 1238 self.update_status(self._workspace_status) 1239 self.display_edit_page() 1240 1241 def save_selected_protein_structure_as_pdb_file(self) -> None: 1242 """Saves selected protein as pdb file.""" 1243 self._view.wait_spinner.start() 1244 file_dialog = QtWidgets.QFileDialog() 1245 desktop_path = QtCore.QStandardPaths.standardLocations(QtCore.QStandardPaths.DesktopLocation)[0] 1246 file_dialog.setDirectory(desktop_path) 1247 file_path, _ = file_dialog.getSaveFileName( 1248 self._view, 1249 "Save protein structure", 1250 "", 1251 "Protein Data Bank File (*.pdb)", 1252 ) 1253 if file_path: 1254 self._active_task = tasks.Task( 1255 target=main_presenter_async.save_selected_protein_structure_as_pdb_file, 1256 args=(self._view.ui.list_edit_project_proteins.currentItem().text(), self._current_project, file_path), 1257 post_func=self.__await_save_selected_protein_structure_as_pdb_file, 1258 ) 1259 self._active_task.start() 1260 else: 1261 self._view.wait_spinner.stop() 1262 1263 def __await_save_selected_protein_structure_as_pdb_file(self, result: tuple) -> None: 1264 self._view.wait_spinner.stop() 1265 if result[0] == exit_codes.EXIT_CODE_ONE_UNKNOWN_ERROR[0]: 1266 basic_boxes.ok( 1267 "Save protein structure", 1268 "Saving the protein as .pdb file failed!", 1269 QtWidgets.QMessageBox.Error, 1270 ) 1271 elif result[0] == exit_codes.EXIT_CODE_ZERO[0]: 1272 basic_boxes.ok( 1273 "Save protein structure", 1274 "The protein was successfully saved as .pdb file.", 1275 QtWidgets.QMessageBox.Information, 1276 ) 1277 else: 1278 basic_boxes.ok( 1279 "Save protein structure", 1280 "Saving the protein as .pdb file failed with an unexpected error!", 1281 QtWidgets.QMessageBox.Error, 1282 ) 1283 self._project_watcher.show_valid_options(self._view.ui) 1284 self.update_status(self._workspace_status) 1285 1286 def rename_selected_protein_structure(self) -> None: 1287 """Opens a new view to rename the selected protein.""" 1288 self._view.wait_spinner.start() 1289 self.tmp_dialog = dialog_rename_protein.DialogRenameProtein(self._workspace_path) 1290 self.tmp_dialog.return_value.connect(self.post_rename_selected_protein_structure) 1291 self.tmp_dialog.show() 1292 1293 def post_rename_selected_protein_structure(self, return_value: tuple) -> None: 1294 """Renames a selected protein structure.""" 1295 if return_value[1] is True: 1296 self._active_task = tasks.Task( 1297 target=main_presenter_async.rename_selected_protein_structure, 1298 args=( 1299 self._view.ui.list_edit_project_proteins.currentItem().text(), 1300 return_value[0], 1301 self._current_project, 1302 ), 1303 post_func=self.__await_post_rename_selected_protein_structure, 1304 ) 1305 self._active_task.start() 1306 else: 1307 self._view.wait_spinner.stop() 1308 1309 def __await_post_rename_selected_protein_structure(self, result: tuple) -> None: 1310 self._init_edit_page() 1311 self._project_watcher.show_valid_options(self._view.ui) 1312 self._view.wait_spinner.stop() 1313 1314 # </editor-fold> 1315 1316 # <editor-fold desc="View project page functions"> 1317 def view_structure(self) -> None: 1318 """Displays the structure of the selected protein in pymol.""" 1319 protein_name = self._view.ui.list_view_project_proteins.currentItem().text() 1320 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 1321 cmd.reinitialize() 1322 self._view.ui.btn_manage_session.show() 1323 try: 1324 self._current_project.search_protein(protein_name).load_protein_pymol_session() 1325 constants.PYSSA_LOGGER.info("Loaded PyMOL session of protein %s", protein_name) 1326 except pymol.CmdException: 1327 constants.PYSSA_LOGGER.error("Error while loading protein in PyMOL!") 1328 return 1329 self.current_session = current_session.CurrentSession( 1330 "protein", 1331 protein_name, 1332 self._current_project.search_protein(protein_name).pymol_session, 1333 ) 1334 print(self.current_session) 1335 1336 # </editor-fold> 1337 1338 # <editor-fold desc="Use project page functions"> 1339 def display_use_page(self) -> None: 1340 """Displays the use project page.""" 1341 self._view.wait_spinner.start() 1342 if self.is_distance_plot_open: 1343 self.distance_plot_dialog.close() 1344 self.is_distance_plot_open = False 1345 1346 self.start_worker_thread( 1347 task_workers.LoadUsePageWorker( 1348 self._workspace_path, 1349 self._current_project.convert_list_of_proteins_to_list_of_protein_infos(), 1350 ), 1351 self.post_display_use_page, 1352 ) 1353 self._init_use_page() 1354 1355 def post_display_use_page(self, return_value) -> None: # noqa: ANN001 1356 """Displays the use project page, after cpu intense task (post thread method). 1357 1358 Args: 1359 return_value: the value which gets returned from the thread process 1360 """ 1361 # this for-loop is necessary for eliminating all proteins which are in the current project from the ones which 1362 # are available 1363 for tmp_item in return_value[0]: 1364 self._view.ui.list_use_available_protein_structures.addItem(tmp_item) 1365 for i in range(self._view.ui.list_use_selected_protein_structures.count()): 1366 self._view.ui.list_use_selected_protein_structures.setCurrentRow(i) 1367 tmp_prot_name = self._view.ui.list_use_selected_protein_structures.currentItem().text() 1368 if tmp_prot_name in return_value[1]: 1369 return_value[1].remove(tmp_prot_name) 1370 1371 for tmp_item in return_value[1]: 1372 self._view.ui.list_use_available_protein_structures.addItem(tmp_item) 1373 for tmp_project_name in return_value[2]: 1374 self._view.ui.list_use_existing_projects.addItem(QtWidgets.QListWidgetItem(tmp_project_name)) 1375 1376 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 14, "Use existing project") 1377 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_use_page) 1378 self._view.wait_spinner.stop() 1379 1380 def pre_create_use_project(self) -> None: 1381 """Sets up the worker for the create_use_project task.""" 1382 QtWidgets.QApplication.setOverrideCursor(Qt.WaitCursor) 1383 # copy proteins in new project 1384 proteins_to_copy = [] 1385 for i in range(self._view.ui.list_use_selected_protein_structures.count()): 1386 self._view.ui.list_use_selected_protein_structures.setCurrentRow(i) 1387 proteins_to_copy.append(self._view.ui.list_use_selected_protein_structures.currentItem().text()) 1388 1389 # <editor-fold desc="Worker setup"> 1390 # --Begin: worker setup 1391 self.tmp_thread = QtCore.QThread() 1392 self.tmp_worker = task_workers.CreateUseProjectWorker(self._workspace_path, proteins_to_copy) 1393 self.tmp_thread = task_workers.setup_worker_for_work(self.tmp_thread, self.tmp_worker, self.create_use_project) 1394 self.tmp_thread.start() 1395 # --End: worker setup 1396 1397 # </editor-fold> 1398 1399 self._view.ui.lbl_current_project_name.setText(self._view.ui.txt_use_project_name.text()) 1400 self._view.status_bar.showMessage(f"Creating new project: {self._view.ui.txt_use_project_name.text()} ...") 1401 # save project folder in current workspace 1402 new_project = project.Project(self._view.ui.txt_use_project_name.text(), self._workspace_path) 1403 # new_project.create_project_tree() 1404 self._current_project = new_project 1405 1406 def create_use_project(self, proteins_for_new_project) -> None: # noqa: ANN001 1407 """Post thread method. 1408 1409 Args: 1410 proteins_for_new_project (list): the proteins which are in the new project 1411 """ 1412 for tmp_protein_obj in proteins_for_new_project: 1413 self._current_project.add_existing_protein(tmp_protein_obj) 1414 self._current_project.serialize_project( 1415 pathlib.Path(f"{self._workspace_path}/{self._current_project.get_project_name()}.xml"), 1416 ) 1417 # shows options which can be done with the data in the project folder 1418 self._project_watcher.current_project = self._current_project 1419 self._project_watcher.on_home_page = False 1420 self._project_watcher.show_valid_options(self._view.ui) 1421 self.project_scanner.project = self._current_project 1422 self._init_use_page() 1423 constants.PYSSA_LOGGER.info( 1424 f"The project {self._current_project.get_project_name()} was successfully created through a use.", 1425 ) 1426 self.display_view_page() 1427 QtWidgets.QApplication.restoreOverrideCursor() 1428 1429 # </editor-fold> 1430 1431 # <editor-fold desc="Import, Export functions"> 1432 def import_project(self) -> None: 1433 """Imports a project.xml into the current workspace.""" 1434 self.last_sidebar_button = styles.color_sidebar_buttons( 1435 self.last_sidebar_button, 1436 self._view.ui.btn_import_project, 1437 ) 1438 file_dialog = QtWidgets.QFileDialog() 1439 desktop_path = QtCore.QStandardPaths.standardLocations(QtCore.QStandardPaths.DesktopLocation)[0] 1440 file_dialog.setDirectory(desktop_path) 1441 file_path, _ = file_dialog.getOpenFileName( 1442 self._view, 1443 "Select a project file to import", 1444 "", 1445 "XML Files (*.xml)", 1446 ) 1447 if file_path: 1448 tmp_project = project.Project("", self._workspace_path) 1449 tmp_project = tmp_project.deserialize_project(pathlib.Path(file_path), self._application_settings) 1450 tmp_project.set_workspace_path(self._workspace_path) 1451 if len(tmp_project.proteins) <= 1: 1452 if self._application_settings.wsl_install == 0: 1453 basic_boxes.ok( 1454 "Create new project", 1455 "Please install local colabfold to import this project!", 1456 QtWidgets.QMessageBox.Warning, 1457 ) 1458 return 1459 elif self._application_settings.local_colabfold == 0: # noqa: RET505 1460 basic_boxes.ok( 1461 "Create new project", 1462 "Please install local colabfold to import this project!", 1463 QtWidgets.QMessageBox.Warning, 1464 ) 1465 return 1466 new_filepath = pathlib.Path(f"{self._workspace_path}/{tmp_project.get_project_name()}.xml") 1467 tmp_project.serialize_project(new_filepath) 1468 self._current_project = self._current_project.deserialize_project(new_filepath, self._application_settings) 1469 constants.PYSSA_LOGGER.info(f"Opening the project {self._current_project.get_project_name()}.") 1470 self._project_watcher.current_project = self._current_project 1471 self.project_scanner.project = self._current_project 1472 constants.PYSSA_LOGGER.info( 1473 f"{self._project_watcher.current_project.get_project_name()} is the current project.", 1474 ) 1475 self._view.ui.lbl_current_project_name.setText(self._current_project.get_project_name()) 1476 self._project_watcher.on_home_page = False 1477 self._project_watcher.show_valid_options(self._view.ui) 1478 self._view.ui.btn_manage_session.show() 1479 self.display_view_page() 1480 basic_boxes.ok( 1481 "Import Project", 1482 "The project was successfully imported.", 1483 QtWidgets.QMessageBox.Information, 1484 ) 1485 1486 def export_current_project(self) -> None: 1487 """Exports the current project to an importable format.""" 1488 if self.is_distance_plot_open: 1489 self.distance_plot_dialog.close() 1490 self.is_distance_plot_open = False 1491 self.last_sidebar_button = styles.color_sidebar_buttons( 1492 self.last_sidebar_button, 1493 self._view.ui.btn_export_project, 1494 ) 1495 file_dialog = QtWidgets.QFileDialog() 1496 desktop_path = QtCore.QStandardPaths.standardLocations(QtCore.QStandardPaths.DesktopLocation)[0] 1497 file_dialog.setDirectory(desktop_path) 1498 file_path, _ = file_dialog.getSaveFileName(self._view, "Save current project", "", "XML Files (*.xml)") 1499 if file_path: 1500 self._current_project.serialize_project(pathlib.Path(file_path)) 1501 basic_boxes.ok( 1502 "Export Project", 1503 "The project was successfully exported.", 1504 QtWidgets.QMessageBox.Information, 1505 ) 1506 1507 # </editor-fold> 1508 1509 # <editor-fold desc="Close project functions"> 1510 def close_project(self) -> None: 1511 """Closes the current project.""" 1512 if self.is_distance_plot_open: 1513 self.distance_plot_dialog.close() 1514 self.is_distance_plot_open = False 1515 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 1516 cmd.reinitialize() 1517 self._view.ui.list_hotspots_choose_protein.clear() 1518 self._project_watcher.on_home_page = True 1519 self._project_watcher.current_project = project.Project("", pathlib.Path("")) 1520 self._project_watcher.show_valid_options(self._view.ui) 1521 self._view.ui.lbl_current_project_name.setText("") 1522 self._init_all_pages() 1523 self.results_name = "" 1524 constants.PYSSA_LOGGER.info(f"The project {self._current_project.get_project_name()} was closed") 1525 self.display_home_page() 1526 1527 # </editor-fold> 1528 1529 # <editor-fold desc="ESMFold Monomer functions"> 1530 def post_predict_esm_monomer(self, output) -> None: # noqa: ANN001 1531 """Post thread method, for the prediction process. 1532 1533 Args: 1534 output (list): the proteins which got predicted 1535 """ 1536 self.block_box_prediction.destroy(True) 1537 for tmp_filename in os.listdir(constants.ESMFOLD_PDB_DIR): 1538 constants.PYSSA_LOGGER.info( 1539 f"Add protein {tmp_filename} to the current project {self._current_project.get_project_name()}", 1540 ) 1541 self._current_project.add_existing_protein( 1542 protein.Protein( 1543 tmp_filename.replace(".pdb", ""), 1544 path_util.FilePath(pathlib.Path(f"{constants.ESMFOLD_PDB_DIR}/{tmp_filename}")), 1545 ), 1546 ) 1547 if len(output) > 0: 1548 formatted_output = ", ".join(output) 1549 basic_boxes.ok( 1550 "ESMFold Prediction", 1551 f"These protein prediction failed: {formatted_output}.", 1552 QtWidgets.QMessageBox.Critical, 1553 ) 1554 else: 1555 basic_boxes.ok("ESMFold Prediction", "The prediction was successful.", QtWidgets.QMessageBox.Information) 1556 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 1557 self.display_view_page() 1558 self._project_watcher.show_valid_options(self._view.ui) 1559 1560 def predict_esm_monomer(self) -> None: 1561 """Sets up the worker to predict the proteins with the ESM-Fold.""" 1562 # <editor-fold desc="Worker setup"> 1563 # --Begin: worker setup 1564 self.tmp_thread = QtCore.QThread() 1565 self.tmp_worker = task_workers.EsmFoldWorker(self._view.ui.table_esm_prot_to_predict) 1566 self.tmp_thread = task_workers.setup_worker_for_work( 1567 self.tmp_thread, 1568 self.tmp_worker, 1569 self.post_predict_esm_monomer, 1570 ) 1571 self.tmp_thread.start() 1572 # --End: worker setup 1573 1574 # </editor-fold> 1575 1576 self.block_box_prediction = QtWidgets.QMessageBox() 1577 self.block_box_prediction = gui_utils.setup_standard_block_box( 1578 self.block_box_prediction, 1579 "Structure Prediction", 1580 "A prediction is currently running.", 1581 ) 1582 # self.block_box_prediction.setStandardButtons(QtWidgets.QMessageBox.NoButton) 1583 # self.block_box_prediction.setIcon(QtWidgets.QMessageBox.Information) 1584 # self.block_box_prediction.setWindowIcon( 1585 # PyQt5.constants.PLUGIN_LOGO_ICON_OBJ) 1586 # styles.set_stylesheet(self.block_box_prediction) 1587 # self.block_box_prediction.setWindowTitle("Structure Prediction") 1588 # self.block_box_prediction.setText("A prediction is currently running.") 1589 self.block_box_prediction.exec_() 1590 1591 # </editor-fold> 1592 1593 # <editor-fold desc="Monomer Local Prediction functions"> 1594 def post_prediction_process(self, an_exit_code: int, an_exit_code_description: str) -> None: 1595 """Process which runs after each prediction job.""" 1596 if an_exit_code == exit_codes.ERROR_WRITING_FASTA_FILES[0]: 1597 self.block_box_prediction.destroy(True) 1598 basic_boxes.ok( 1599 "Prediction", 1600 "Prediction failed because there was an error writing the fasta file(s)!", 1601 QtWidgets.QMessageBox.Critical, 1602 ) 1603 self.display_view_page() 1604 self._project_watcher.show_valid_options(self._view.ui) 1605 constants.PYSSA_LOGGER.error(f"Prediction ended with exit code {an_exit_code}: {an_exit_code_description}") 1606 elif an_exit_code == exit_codes.ERROR_FASTA_FILES_NOT_FOUND[0]: 1607 self.block_box_prediction.destroy(True) 1608 basic_boxes.ok( 1609 "Prediction", 1610 "Prediction failed because the fasta file(s) could not be found!", 1611 QtWidgets.QMessageBox.Critical, 1612 ) 1613 self.display_view_page() 1614 self._project_watcher.show_valid_options(self._view.ui) 1615 constants.PYSSA_LOGGER.error(f"Prediction ended with exit code {an_exit_code}: {an_exit_code_description}") 1616 elif an_exit_code == exit_codes.ERROR_PREDICTION_FAILED[0]: 1617 self.block_box_prediction.destroy(True) 1618 basic_boxes.ok( 1619 "Prediction", 1620 "Prediction failed because a subprocess failed!", 1621 QtWidgets.QMessageBox.Critical, 1622 ) 1623 self.display_view_page() 1624 self._project_watcher.show_valid_options(self._view.ui) 1625 constants.PYSSA_LOGGER.error(f"Prediction ended with exit code {an_exit_code}: {an_exit_code_description}") 1626 elif an_exit_code == exit_codes.EXIT_CODE_ONE_UNKNOWN_ERROR[0]: 1627 self.block_box_prediction.destroy(True) 1628 basic_boxes.ok( 1629 "Prediction", 1630 "Prediction failed because of an unknown error!", 1631 QtWidgets.QMessageBox.Critical, 1632 ) 1633 self.display_view_page() 1634 self._project_watcher.show_valid_options(self._view.ui) 1635 constants.PYSSA_LOGGER.error(f"Prediction ended with exit code {an_exit_code}: {an_exit_code_description}") 1636 elif an_exit_code == exit_codes.EXIT_CODE_ZERO[0]: 1637 # Prediction was successful 1638 if self.prediction_type == constants.PREDICTION_TYPE_PRED: 1639 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 1640 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 1641 self.block_box_prediction.destroy(True) 1642 basic_boxes.ok( 1643 "Structure prediction", 1644 "All structure predictions are done. Go to View to check the new proteins.", 1645 QtWidgets.QMessageBox.Information, 1646 ) 1647 constants.PYSSA_LOGGER.info("All structure predictions are done.") 1648 self._project_watcher.show_valid_options(self._view.ui) 1649 self._init_local_pred_mono_page() 1650 self._init_local_pred_multi_page() 1651 self.display_view_page() 1652 elif self.prediction_type == constants.PREDICTION_TYPE_PRED_MONO_ANALYSIS: 1653 # executes if monomers were successfully predicted 1654 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 1655 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 1656 constants.PYSSA_LOGGER.info("All structure predictions are done.") 1657 constants.PYSSA_LOGGER.info("Begin analysis process.") 1658 constants.PYSSA_LOGGER.debug( 1659 f"Thread count before analysis worker: {self.threadpool.activeThreadCount()}", 1660 ) 1661 1662 # self.worker_analysis = workers.AnalysisWorkerPool( 1663 # self._view.ui.list_pred_analysis_mono_overview, self._view.ui.cb_pred_analysis_mono_images, 1664 # self._view.status_bar, self._current_project, self._application_settings, self._init_mono_pred_analysis_page) 1665 constants.PYSSA_LOGGER.info("Thread started for analysis process.") 1666 # self.threadpool.start(self.worker_analysis) 1667 constants.PYSSA_LOGGER.debug( 1668 f"Thread count after analysis worker: {self.threadpool.activeThreadCount()}", 1669 ) 1670 1671 # <editor-fold desc="Worker setup"> 1672 # TODO: test code below 1673 # --Begin: worker setup 1674 self.tmp_thread = QtCore.QThread() 1675 self.tmp_worker = task_workers.DistanceAnalysisWorker( 1676 self._view.ui.list_pred_analysis_mono_overview, 1677 self._view.ui.cb_pred_analysis_mono_images, 1678 self._view.status_bar, 1679 self._current_project, 1680 self._application_settings, 1681 self._init_mono_pred_analysis_page, 1682 ) 1683 self.tmp_thread = task_workers.setup_worker_for_work( 1684 self.tmp_thread, 1685 self.tmp_worker, 1686 self.display_view_page, 1687 ) 1688 self.tmp_worker.finished.connect(self.post_analysis_process) 1689 self.tmp_thread.start() 1690 # --End: worker setup 1691 1692 # </editor-fold> 1693 1694 if not os.path.exists(constants.SCRATCH_DIR_ANALYSIS): 1695 os.mkdir(constants.SCRATCH_DIR_ANALYSIS) 1696 self.block_box_prediction.destroy(True) 1697 self.block_box_analysis.exec_() 1698 self.display_view_page() 1699 self._project_watcher.show_valid_options(self._view.ui) 1700 elif self.prediction_type == constants.PREDICTION_TYPE_PRED_MULTI_ANALYSIS: 1701 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 1702 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 1703 constants.PYSSA_LOGGER.info("All structure predictions are done.") 1704 constants.PYSSA_LOGGER.info("Begin analysis process.") 1705 constants.PYSSA_LOGGER.debug( 1706 f"Thread count before analysis worker: {self.threadpool.activeThreadCount()}", 1707 ) 1708 1709 # self.worker_analysis = workers.AnalysisWorkerPool( 1710 # self._view.ui.list_pred_analysis_multi_overview, self._view.ui.cb_pred_analysis_multi_images, 1711 # self._view.status_bar, self._current_project, self._application_settings, self._init_multi_pred_analysis_page) 1712 constants.PYSSA_LOGGER.info("Thread started for analysis process.") 1713 # self.threadpool.start(self.worker_analysis) 1714 constants.PYSSA_LOGGER.debug( 1715 f"Thread count after analysis worker: {self.threadpool.activeThreadCount()}", 1716 ) 1717 1718 # <editor-fold desc="Worker setup"> 1719 # TODO: test code below 1720 # --Begin: worker setup 1721 self.tmp_thread = QtCore.QThread() 1722 self.tmp_worker = task_workers.DistanceAnalysisWorker( 1723 self._view.ui.list_pred_analysis_multi_overview, 1724 self._view.ui.cb_pred_analysis_multi_images, 1725 self._view.status_bar, 1726 self._current_project, 1727 self._application_settings, 1728 self._init_multi_pred_analysis_page, 1729 ) 1730 self.tmp_thread = task_workers.setup_worker_for_work( 1731 self.tmp_thread, 1732 self.tmp_worker, 1733 self.display_view_page, 1734 ) 1735 self.tmp_worker.finished.connect(self.post_analysis_process) 1736 self.tmp_thread.start() 1737 # --End: worker setup 1738 1739 # </editor-fold> 1740 1741 if not os.path.exists(constants.SCRATCH_DIR_ANALYSIS): 1742 os.mkdir(constants.SCRATCH_DIR_ANALYSIS) 1743 self.block_box_prediction.destroy(True) 1744 self.block_box_analysis.exec_() 1745 self.display_view_page() 1746 self._project_watcher.show_valid_options(self._view.ui) 1747 try: 1748 shutil.rmtree(pathlib.Path(f"{constants.SCRATCH_DIR}/local_predictions")) 1749 except Exception as e: 1750 constants.PYSSA_LOGGER.warning(f"Local predictions scratch path could not be deleted. {e}") 1751 1752 def predict_local_monomer(self) -> None: 1753 """Sets tup the worker for the prediction with the colabfold.""" 1754 self._view.wait_spinner.start() 1755 self.prediction_type = constants.PREDICTION_TYPE_PRED 1756 constants.PYSSA_LOGGER.info("Begin prediction process.") 1757 self.update_status("Begin prediction process ...") 1758 predictions: list[ 1759 prediction_protein_info.PredictionProteinInfo 1760 ] = prediction_util.get_prediction_name_and_seq_from_table(self._view.ui.table_pred_mono_prot_to_predict) 1761 1762 self._active_task = tasks.Task( 1763 target=main_presenter_async.predict_protein_with_colabfold, 1764 args=( 1765 predictions, 1766 self.prediction_configuration, 1767 self._current_project, 1768 ), 1769 post_func=self.__await_predict_protein_with_colabfold, 1770 ) 1771 self._active_task.start() 1772 1773 self.block_box_prediction = QtWidgets.QMessageBox() 1774 self.block_box_prediction.setIcon(QtWidgets.QMessageBox.Information) 1775 self.block_box_prediction.setWindowIcon(QtGui.QIcon(constants.PLUGIN_LOGO_FILEPATH)) 1776 styles.set_stylesheet(self.block_box_prediction) 1777 self.block_box_prediction.setWindowTitle("Structure Prediction") 1778 self.block_box_prediction.setText("A prediction is currently running.") 1779 btn_abort = self.block_box_prediction.addButton("Abort", QtWidgets.QMessageBox.ActionRole) 1780 self.block_box_prediction.exec_() 1781 if self.block_box_prediction.clickedButton() == btn_abort: 1782 self.abort_prediction() 1783 self.block_box_prediction.close() 1784 self._view.wait_spinner.stop() 1785 return 1786 else: # noqa: RET505 1787 self.block_box_prediction.close() 1788 self._view.wait_spinner.stop() 1789 1790 def __await_predict_protein_with_colabfold(self, result: tuple) -> None: 1791 """Process which runs after each prediction job.""" 1792 tmp_exit_code = result[0] 1793 tmp_exit_code_description = [1] 1794 if tmp_exit_code == exit_codes.ERROR_WRITING_FASTA_FILES[0]: 1795 self.block_box_prediction.destroy(True) 1796 basic_boxes.ok( 1797 "Prediction", 1798 "Prediction failed because there was an error writing the fasta file(s)!", 1799 QtWidgets.QMessageBox.Critical, 1800 ) 1801 self.display_view_page() 1802 self._project_watcher.show_valid_options(self._view.ui) 1803 constants.PYSSA_LOGGER.error( 1804 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 1805 ) 1806 elif tmp_exit_code == exit_codes.ERROR_FASTA_FILES_NOT_FOUND[0]: 1807 self.block_box_prediction.destroy(True) 1808 basic_boxes.ok( 1809 "Prediction", 1810 "Prediction failed because the fasta file(s) could not be found!", 1811 QtWidgets.QMessageBox.Critical, 1812 ) 1813 self.display_view_page() 1814 self._project_watcher.show_valid_options(self._view.ui) 1815 constants.PYSSA_LOGGER.error( 1816 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 1817 ) 1818 elif tmp_exit_code == exit_codes.ERROR_PREDICTION_FAILED[0]: 1819 self.block_box_prediction.destroy(True) 1820 basic_boxes.ok( 1821 "Prediction", 1822 "Prediction failed because a subprocess failed!", 1823 QtWidgets.QMessageBox.Critical, 1824 ) 1825 self.display_view_page() 1826 self._project_watcher.show_valid_options(self._view.ui) 1827 constants.PYSSA_LOGGER.error( 1828 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 1829 ) 1830 elif tmp_exit_code == exit_codes.EXIT_CODE_ONE_UNKNOWN_ERROR[0]: 1831 self.block_box_prediction.destroy(True) 1832 basic_boxes.ok( 1833 "Prediction", 1834 "Prediction failed because of an unknown error!", 1835 QtWidgets.QMessageBox.Critical, 1836 ) 1837 self.display_view_page() 1838 self._project_watcher.show_valid_options(self._view.ui) 1839 constants.PYSSA_LOGGER.error( 1840 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 1841 ) 1842 elif tmp_exit_code == exit_codes.EXIT_CODE_ZERO[0]: 1843 # Prediction was successful 1844 if self.prediction_type == constants.PREDICTION_TYPE_PRED: 1845 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 1846 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 1847 self.block_box_prediction.destroy(True) 1848 basic_boxes.ok( 1849 "Structure prediction", 1850 "All structure predictions are done. Go to View to check the new proteins.", 1851 QtWidgets.QMessageBox.Information, 1852 ) 1853 constants.PYSSA_LOGGER.info("All structure predictions are done.") 1854 self._project_watcher.show_valid_options(self._view.ui) 1855 self._init_local_pred_mono_page() 1856 self._init_local_pred_multi_page() 1857 self.display_view_page() 1858 self._view.wait_spinner.stop() 1859 1860 def abort_prediction(self) -> None: 1861 """Aborts the running prediction.""" 1862 constants.PYSSA_LOGGER.info("Structure prediction process was aborted manually.") 1863 subprocess.run(["wsl", "--shutdown"]) 1864 constants.PYSSA_LOGGER.info("Shutdown of wsl environment.") 1865 filesystem_io.FilesystemCleaner.clean_prediction_scratch_folder() 1866 constants.PYSSA_LOGGER.info("Cleaned scratch directory.") 1867 basic_boxes.ok("Abort prediction", "The structure prediction was aborted.", QtWidgets.QMessageBox.Information) 1868 self.last_sidebar_button = styles.color_sidebar_buttons( 1869 self.last_sidebar_button, 1870 self._view.ui.btn_prediction_abort, 1871 ) 1872 self._project_watcher.show_valid_options(self._view.ui) 1873 1874 # </editor-fold> 1875 1876 # <editor-fold desc="Multimer Local Prediction functions"> 1877 def predict_local_multimer(self) -> None: 1878 """Sets up the worker for the prediction with the colabfold.""" 1879 self._view.wait_spinner.start() 1880 self.prediction_type = constants.PREDICTION_TYPE_PRED 1881 constants.PYSSA_LOGGER.info("Begin multimer prediction process.") 1882 self.update_status("Begin prediction process ...") 1883 predictions: list[ 1884 prediction_protein_info.PredictionProteinInfo 1885 ] = prediction_util.get_prediction_name_and_seq_from_table(self._view.ui.table_pred_multi_prot_to_predict) 1886 1887 self._active_task = tasks.Task( 1888 target=main_presenter_async.predict_protein_with_colabfold, 1889 args=( 1890 predictions, 1891 self.prediction_configuration, 1892 self._current_project, 1893 ), 1894 post_func=self.__await_predict_protein_with_colabfold, 1895 ) 1896 self._active_task.start() 1897 1898 self.block_box_prediction = QtWidgets.QMessageBox() 1899 self.block_box_prediction.setIcon(QtWidgets.QMessageBox.Information) 1900 self.block_box_prediction.setWindowIcon(QtGui.QIcon(constants.PLUGIN_LOGO_FILEPATH)) 1901 styles.set_stylesheet(self.block_box_prediction) 1902 self.block_box_prediction.setWindowTitle("Structure Prediction") 1903 self.block_box_prediction.setText("A prediction is currently running.") 1904 btn_abort = self.block_box_prediction.addButton("Abort", QtWidgets.QMessageBox.ActionRole) 1905 self.block_box_prediction.exec_() 1906 if self.block_box_prediction.clickedButton() == btn_abort: 1907 self.abort_prediction() 1908 self.block_box_prediction.close() 1909 self._view.wait_spinner.stop() 1910 else: 1911 self.block_box_prediction.close() 1912 self._view.wait_spinner.stop() 1913 1914 # </editor-fold> 1915 1916 # <editor-fold desc="Monomer Prediction + Analysis functions"> 1917 def start_monomer_prediction_analysis(self) -> None: 1918 """Sets up the worker for the prediction of the proteins.""" 1919 self._view.wait_spinner.start() 1920 self.prediction_type = constants.PREDICTION_TYPE_PRED_MONO_ANALYSIS 1921 constants.PYSSA_LOGGER.info("Begin prediction process.") 1922 self.update_status("Begin prediction process ...") 1923 predictions: list[ 1924 prediction_protein_info.PredictionProteinInfo 1925 ] = prediction_util.get_prediction_name_and_seq_from_table( 1926 self._view.ui.table_pred_analysis_mono_prot_to_predict, 1927 ) 1928 1929 self._active_task = tasks.Task( 1930 target=main_presenter_async.predict_protein_with_colabfold, 1931 args=( 1932 predictions, 1933 self.prediction_configuration, 1934 self._current_project, 1935 ), 1936 post_func=self.__await_monomer_prediction_for_subsequent_analysis, 1937 ) 1938 self._active_task.start() 1939 1940 self.block_box_prediction = QtWidgets.QMessageBox() 1941 self.block_box_prediction.setIcon(QtWidgets.QMessageBox.Information) 1942 self.block_box_prediction.setWindowIcon(QtGui.QIcon(constants.PLUGIN_LOGO_FILEPATH)) 1943 styles.set_stylesheet(self.block_box_prediction) 1944 self.block_box_prediction.setWindowTitle("Structure Prediction") 1945 self.block_box_prediction.setText("A prediction is currently running.") 1946 btn_abort = self.block_box_prediction.addButton("Abort", QtWidgets.QMessageBox.ActionRole) 1947 self.block_box_prediction.exec_() 1948 if self.block_box_prediction.clickedButton() == btn_abort: 1949 self.abort_prediction() 1950 self.block_box_prediction.close() 1951 self._view.wait_spinner.stop() 1952 else: 1953 self.block_box_prediction.close() 1954 self._view.wait_spinner.stop() 1955 1956 def __await_monomer_prediction_for_subsequent_analysis(self, result: tuple) -> None: 1957 tmp_exit_code = result[0] 1958 tmp_exit_code_description = [1] 1959 if tmp_exit_code == exit_codes.EXIT_CODE_ZERO[0]: 1960 # Prediction was successful 1961 self.block_box_prediction.destroy(True) 1962 constants.PYSSA_LOGGER.info("All structure predictions are done.") 1963 self.update_status("All structure predictions are done.") 1964 constants.PYSSA_LOGGER.info("Begin analysis process.") 1965 self.update_status("Begin analysis process ...") 1966 1967 tmp_raw_analysis_run_names: list = [] 1968 for row_no in range(self._view.ui.list_pred_analysis_mono_overview.count()): 1969 tmp_raw_analysis_run_names.append(self._view.ui.list_pred_analysis_mono_overview.item(row_no).text()) 1970 1971 self._active_task = tasks.Task( 1972 target=main_presenter_async.run_distance_analysis, 1973 args=( 1974 tmp_raw_analysis_run_names, 1975 self._current_project, 1976 self._application_settings, 1977 self._view.ui.cb_pred_analysis_mono_images.isChecked(), 1978 ), 1979 post_func=self.post_analysis_process, 1980 ) 1981 self._active_task.start() 1982 1983 if not os.path.exists(constants.SCRATCH_DIR_ANALYSIS): 1984 os.mkdir(constants.SCRATCH_DIR_ANALYSIS) 1985 self.block_box_analysis.exec_() 1986 self.display_view_page() 1987 1988 elif tmp_exit_code == exit_codes.ERROR_WRITING_FASTA_FILES[0]: 1989 self.block_box_prediction.destroy(True) 1990 basic_boxes.ok( 1991 "Prediction", 1992 "Prediction failed because there was an error writing the fasta file(s)!", 1993 QtWidgets.QMessageBox.Critical, 1994 ) 1995 self.display_view_page() 1996 self._project_watcher.show_valid_options(self._view.ui) 1997 constants.PYSSA_LOGGER.error( 1998 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 1999 ) 2000 self._view.wait_spinner.stop() 2001 elif tmp_exit_code == exit_codes.ERROR_FASTA_FILES_NOT_FOUND[0]: 2002 self.block_box_prediction.destroy(True) 2003 basic_boxes.ok( 2004 "Prediction", 2005 "Prediction failed because the fasta file(s) could not be found!", 2006 QtWidgets.QMessageBox.Critical, 2007 ) 2008 self.display_view_page() 2009 self._project_watcher.show_valid_options(self._view.ui) 2010 constants.PYSSA_LOGGER.error( 2011 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 2012 ) 2013 self._view.wait_spinner.stop() 2014 elif tmp_exit_code == exit_codes.ERROR_PREDICTION_FAILED[0]: 2015 self.block_box_prediction.destroy(True) 2016 basic_boxes.ok( 2017 "Prediction", 2018 "Prediction failed because a subprocess failed!", 2019 QtWidgets.QMessageBox.Critical, 2020 ) 2021 self.display_view_page() 2022 self._project_watcher.show_valid_options(self._view.ui) 2023 constants.PYSSA_LOGGER.error( 2024 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 2025 ) 2026 self._view.wait_spinner.stop() 2027 elif tmp_exit_code == exit_codes.EXIT_CODE_ONE_UNKNOWN_ERROR[0]: 2028 self.block_box_prediction.destroy(True) 2029 basic_boxes.ok( 2030 "Prediction", 2031 "Prediction failed because of an unknown error!", 2032 QtWidgets.QMessageBox.Critical, 2033 ) 2034 self.display_view_page() 2035 self._project_watcher.show_valid_options(self._view.ui) 2036 constants.PYSSA_LOGGER.error( 2037 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 2038 ) 2039 self._view.wait_spinner.stop() 2040 2041 def mono_pred_analysis_structure_analysis_next_2(self) -> None: 2042 """Shows the gui elements for the chain selection of protein 1.""" 2043 self._view.wait_spinner.start() 2044 tmp_proteins_to_predict: list[str] = [] 2045 for i in range(self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount()): 2046 tmp_proteins_to_predict.append( 2047 self._view.ui.table_pred_analysis_mono_prot_to_predict.verticalHeaderItem(i).text(), 2048 ) 2049 self._active_task = tasks.Task( 2050 target=main_presenter_async.check_chains_for_subsequent_analysis, 2051 args=( 2052 self._view.ui.box_pred_analysis_mono_prot_struct_1.currentText(), 2053 self._view.ui.box_pred_analysis_mono_prot_struct_2.currentText(), 2054 self._current_project, 2055 tmp_proteins_to_predict, 2056 ), 2057 post_func=self.__await_mono_pred_analysis_structure_analysis_next_2, 2058 ) 2059 self._active_task.start() 2060 2061 def __await_mono_pred_analysis_structure_analysis_next_2(self, result: tuple) -> None: 2062 _, tmp_analysis_name = result 2063 if tmp_analysis_name != "": 2064 gui_elements_to_show = [ 2065 self._view.ui.btn_pred_analysis_mono_remove, 2066 self._view.ui.btn_pred_analysis_mono_add, 2067 self._view.ui.lbl_pred_analysis_mono_overview, 2068 self._view.ui.list_pred_analysis_mono_overview, 2069 self._view.ui.lbl_pred_analysis_mono_images, 2070 self._view.ui.cb_pred_analysis_mono_images, 2071 self._view.ui.btn_pred_analysis_mono_start, 2072 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 2073 ] 2074 gui_elements_to_hide = [ 2075 self._view.ui.box_pred_analysis_mono_prot_struct_1, 2076 self._view.ui.box_pred_analysis_mono_prot_struct_2, 2077 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 2078 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 2079 self._view.ui.lbl_analysis_batch_vs_2, 2080 self._view.ui.lbl_pred_analysis_mono_ref_chains, 2081 self._view.ui.list_pred_analysis_mono_ref_chains, 2082 self._view.ui.lbl_pred_analysis_mono_model_chains, 2083 self._view.ui.list_pred_analysis_mono_model_chains, 2084 self._view.ui.btn_pred_analysis_mono_back_3, 2085 self._view.ui.btn_pred_analysis_mono_next_2, 2086 self._view.ui.btn_pred_analysis_mono_back_4, 2087 self._view.ui.btn_pred_analysis_mono_next_3, 2088 self._view.ui.btn_pred_analysis_mono_back_5, 2089 self._view.ui.btn_pred_analysis_mono_next_4, 2090 ] 2091 gui_utils.show_gui_elements(gui_elements_to_show) 2092 gui_utils.hide_gui_elements(gui_elements_to_hide) 2093 item = QtWidgets.QListWidgetItem(tmp_analysis_name) 2094 self._view.ui.list_pred_analysis_mono_overview.addItem(item) 2095 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(False) 2096 else: 2097 gui_elements_to_show = [ 2098 self._view.ui.lbl_pred_analysis_mono_overview, 2099 self._view.ui.list_pred_analysis_mono_overview, 2100 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 2101 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 2102 self._view.ui.lbl_analysis_batch_vs_2, 2103 self._view.ui.lbl_pred_analysis_mono_ref_chains, 2104 self._view.ui.list_pred_analysis_mono_ref_chains, 2105 self._view.ui.btn_pred_analysis_mono_back_4, 2106 self._view.ui.btn_pred_analysis_mono_next_3, 2107 ] 2108 gui_elements_to_hide = [ 2109 self._view.ui.btn_pred_analysis_mono_remove, 2110 self._view.ui.btn_pred_analysis_mono_add, 2111 self._view.ui.box_pred_analysis_mono_prot_struct_1, 2112 self._view.ui.box_pred_analysis_mono_prot_struct_2, 2113 self._view.ui.btn_pred_analysis_mono_back_3, 2114 self._view.ui.btn_pred_analysis_mono_next_2, 2115 self._view.ui.lbl_pred_analysis_mono_model_chains, 2116 self._view.ui.list_pred_analysis_mono_model_chains, 2117 self._view.ui.btn_pred_analysis_mono_back_5, 2118 self._view.ui.btn_pred_analysis_mono_next_4, 2119 self._view.ui.lbl_pred_analysis_mono_images, 2120 self._view.ui.cb_pred_analysis_mono_images, 2121 self._view.ui.btn_pred_analysis_mono_start, 2122 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 2123 ] 2124 gui_utils.show_gui_elements(gui_elements_to_show) 2125 gui_utils.hide_gui_elements(gui_elements_to_hide) 2126 self._view.ui.lbl_pred_analysis_mono_prot_struct_1.setText( 2127 self._view.ui.box_pred_analysis_mono_prot_struct_1.currentText(), 2128 ) 2129 self._view.ui.lbl_pred_analysis_mono_prot_struct_2.setText( 2130 self._view.ui.box_pred_analysis_mono_prot_struct_2.currentText(), 2131 ) 2132 self._view.ui.list_pred_analysis_mono_ref_chains.clear() 2133 self._view.ui.btn_pred_analysis_mono_next_3.setEnabled(False) 2134 self._view.ui.list_pred_analysis_mono_ref_chains.setEnabled(True) 2135 2136 for i in range(self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount()): 2137 if ( 2138 self._view.ui.table_pred_analysis_mono_prot_to_predict.verticalHeaderItem(i).text() 2139 == self._view.ui.box_pred_analysis_mono_prot_struct_1.currentText() 2140 ): 2141 self._view.ui.list_pred_analysis_mono_ref_chains.addItem( 2142 self._view.ui.table_pred_analysis_mono_prot_to_predict.item(i, 0).text(), 2143 ) 2144 if self._view.ui.list_pred_analysis_mono_ref_chains.count() == 0: 2145 tmp_protein = self._current_project.search_protein( 2146 self._view.ui.box_pred_analysis_mono_prot_struct_1.currentText(), 2147 ) 2148 for tmp_chain in tmp_protein.chains: 2149 if tmp_chain.chain_type == "protein_chain": 2150 self._view.ui.list_pred_analysis_mono_ref_chains.addItem(tmp_chain.chain_letter) 2151 if self._view.ui.list_pred_analysis_mono_ref_chains.count() == 1: 2152 self._view.ui.lbl_pred_analysis_mono_ref_chains.setText( 2153 f"Select chain in protein structure {self._view.ui.lbl_pred_analysis_mono_prot_struct_1.text()}.", 2154 ) 2155 else: 2156 self._view.ui.lbl_pred_analysis_mono_ref_chains.setText( 2157 f"Select chains in protein structure {self._view.ui.lbl_pred_analysis_mono_prot_struct_1.text()}.", 2158 ) 2159 self._view.wait_spinner.stop() 2160 2161 # </editor-fold> 2162 2163 # <editor-fold desc="Multimer Prediction + Analysis functions"> 2164 def start_multimer_prediction_analysis(self) -> None: 2165 """Sets up the prediction process.""" 2166 self._view.wait_spinner.start() 2167 self.prediction_type = constants.PREDICTION_TYPE_PRED_MULTI_ANALYSIS 2168 constants.PYSSA_LOGGER.info("Begin prediction process.") 2169 self.update_status("Begin prediction process ...") 2170 predictions: list[ 2171 prediction_protein_info.PredictionProteinInfo 2172 ] = prediction_util.get_prediction_name_and_seq_from_table( 2173 self._view.ui.table_pred_analysis_multi_prot_to_predict, 2174 ) 2175 2176 self._active_task = tasks.Task( 2177 target=main_presenter_async.predict_protein_with_colabfold, 2178 args=( 2179 predictions, 2180 self.prediction_configuration, 2181 self._current_project, 2182 ), 2183 post_func=self.__await_multimer_prediction_for_subsequent_analysis, 2184 ) 2185 self._active_task.start() 2186 2187 self.block_box_prediction = QtWidgets.QMessageBox() 2188 self.block_box_prediction.setIcon(QtWidgets.QMessageBox.Information) 2189 self.block_box_prediction.setWindowIcon(QtGui.QIcon(constants.PLUGIN_LOGO_FILEPATH)) 2190 styles.set_stylesheet(self.block_box_prediction) 2191 self.block_box_prediction.setWindowTitle("Structure Prediction") 2192 self.block_box_prediction.setText("A prediction is currently running.") 2193 btn_abort = self.block_box_prediction.addButton("Abort", QtWidgets.QMessageBox.ActionRole) 2194 self.block_box_prediction.exec_() 2195 if self.block_box_prediction.clickedButton() == btn_abort: 2196 self.abort_prediction() 2197 self.block_box_prediction.close() 2198 self._view.wait_spinner.stop() 2199 else: 2200 self.block_box_prediction.close() 2201 self._view.wait_spinner.stop() 2202 2203 def __await_multimer_prediction_for_subsequent_analysis(self, result: tuple) -> None: 2204 tmp_exit_code = result[0] 2205 tmp_exit_code_description = [1] 2206 if tmp_exit_code == exit_codes.EXIT_CODE_ZERO[0]: 2207 # Prediction was successful 2208 self.block_box_prediction.destroy(True) 2209 constants.PYSSA_LOGGER.info("All structure predictions are done.") 2210 self.update_status("All structure predictions are done.") 2211 constants.PYSSA_LOGGER.info("Begin analysis process.") 2212 self.update_status("Begin analysis process ...") 2213 tmp_raw_analysis_run_names: list = [] 2214 for row_no in range(self._view.ui.list_pred_analysis_multi_overview.count()): 2215 tmp_raw_analysis_run_names.append(self._view.ui.list_pred_analysis_multi_overview.item(row_no).text()) 2216 2217 self._active_task = tasks.Task( 2218 target=main_presenter_async.run_distance_analysis, 2219 args=( 2220 tmp_raw_analysis_run_names, 2221 self._current_project, 2222 self._application_settings, 2223 self._view.ui.cb_pred_analysis_multi_images.isChecked(), 2224 ), 2225 post_func=self.post_analysis_process, 2226 ) 2227 self._active_task.start() 2228 2229 if not os.path.exists(constants.SCRATCH_DIR_ANALYSIS): 2230 os.mkdir(constants.SCRATCH_DIR_ANALYSIS) 2231 self.block_box_analysis.exec_() 2232 self.display_view_page() 2233 2234 elif tmp_exit_code == exit_codes.ERROR_WRITING_FASTA_FILES[0]: 2235 self.block_box_prediction.destroy(True) 2236 basic_boxes.ok( 2237 "Prediction", 2238 "Prediction failed because there was an error writing the fasta file(s)!", 2239 QtWidgets.QMessageBox.Critical, 2240 ) 2241 self.display_view_page() 2242 self._project_watcher.show_valid_options(self._view.ui) 2243 constants.PYSSA_LOGGER.error( 2244 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 2245 ) 2246 self._view.wait_spinner.stop() 2247 elif tmp_exit_code == exit_codes.ERROR_FASTA_FILES_NOT_FOUND[0]: 2248 self.block_box_prediction.destroy(True) 2249 basic_boxes.ok( 2250 "Prediction", 2251 "Prediction failed because the fasta file(s) could not be found!", 2252 QtWidgets.QMessageBox.Critical, 2253 ) 2254 self.display_view_page() 2255 self._project_watcher.show_valid_options(self._view.ui) 2256 constants.PYSSA_LOGGER.error( 2257 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 2258 ) 2259 self._view.wait_spinner.stop() 2260 elif tmp_exit_code == exit_codes.ERROR_PREDICTION_FAILED[0]: 2261 self.block_box_prediction.destroy(True) 2262 basic_boxes.ok( 2263 "Prediction", 2264 "Prediction failed because a subprocess failed!", 2265 QtWidgets.QMessageBox.Critical, 2266 ) 2267 self.display_view_page() 2268 self._project_watcher.show_valid_options(self._view.ui) 2269 constants.PYSSA_LOGGER.error( 2270 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 2271 ) 2272 self._view.wait_spinner.stop() 2273 elif tmp_exit_code == exit_codes.EXIT_CODE_ONE_UNKNOWN_ERROR[0]: 2274 self.block_box_prediction.destroy(True) 2275 basic_boxes.ok( 2276 "Prediction", 2277 "Prediction failed because of an unknown error!", 2278 QtWidgets.QMessageBox.Critical, 2279 ) 2280 self.display_view_page() 2281 self._project_watcher.show_valid_options(self._view.ui) 2282 constants.PYSSA_LOGGER.error( 2283 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 2284 ) 2285 self._view.wait_spinner.stop() 2286 2287 def multi_pred_analysis_structure_analysis_next_2(self) -> None: 2288 """Shows the gui elements to select the chains in protein 1.""" 2289 self._view.wait_spinner.start() 2290 tmp_proteins_to_predict: list[str] = [] 2291 for i in range(self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount()): 2292 tmp_proteins_to_predict.append( 2293 self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem(i).text(), 2294 ) 2295 self._active_task = tasks.Task( 2296 target=main_presenter_async.check_chains_for_subsequent_analysis, 2297 args=( 2298 self._view.ui.box_pred_analysis_multi_prot_struct_1.currentText(), 2299 self._view.ui.box_pred_analysis_multi_prot_struct_2.currentText(), 2300 self._current_project, 2301 tmp_proteins_to_predict, 2302 ), 2303 post_func=self.__await_multi_pred_analysis_structure_analysis_next_2, 2304 ) 2305 self._active_task.start() 2306 2307 def __await_multi_pred_analysis_structure_analysis_next_2(self, result: tuple) -> None: 2308 # fixme: something is not quite right with the detection of the chains! 2309 _, tmp_analysis_name = result 2310 if tmp_analysis_name != "": 2311 gui_elements_to_show = [ 2312 self._view.ui.btn_pred_analysis_multi_remove, 2313 self._view.ui.btn_pred_analysis_multi_add, 2314 self._view.ui.lbl_pred_analysis_multi_overview, 2315 self._view.ui.list_pred_analysis_multi_overview, 2316 self._view.ui.lbl_pred_analysis_multi_images, 2317 self._view.ui.cb_pred_analysis_multi_images, 2318 self._view.ui.btn_pred_analysis_multi_start, 2319 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 2320 ] 2321 gui_elements_to_hide = [ 2322 self._view.ui.box_pred_analysis_multi_prot_struct_1, 2323 self._view.ui.box_pred_analysis_multi_prot_struct_2, 2324 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 2325 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 2326 self._view.ui.lbl_analysis_batch_vs_3, 2327 self._view.ui.lbl_pred_analysis_multi_ref_chains, 2328 self._view.ui.list_pred_analysis_multi_ref_chains, 2329 self._view.ui.lbl_pred_analysis_multi_model_chains, 2330 self._view.ui.list_pred_analysis_multi_model_chains, 2331 self._view.ui.btn_pred_analysis_multi_back_3, 2332 self._view.ui.btn_pred_analysis_multi_next_2, 2333 self._view.ui.btn_pred_analysis_multi_back_4, 2334 self._view.ui.btn_pred_analysis_multi_next_3, 2335 self._view.ui.btn_pred_analysis_multi_back_5, 2336 self._view.ui.btn_pred_analysis_multi_next_4, 2337 ] 2338 gui_utils.show_gui_elements(gui_elements_to_show) 2339 gui_utils.hide_gui_elements(gui_elements_to_hide) 2340 item = QtWidgets.QListWidgetItem(tmp_analysis_name) 2341 self._view.ui.list_pred_analysis_multi_overview.addItem(item) 2342 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(False) 2343 else: 2344 gui_elements_to_show = [ 2345 self._view.ui.lbl_pred_analysis_multi_overview, 2346 self._view.ui.list_pred_analysis_multi_overview, 2347 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 2348 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 2349 self._view.ui.lbl_analysis_batch_vs_3, 2350 self._view.ui.lbl_pred_analysis_multi_ref_chains, 2351 self._view.ui.list_pred_analysis_multi_ref_chains, 2352 self._view.ui.btn_pred_analysis_multi_back_4, 2353 self._view.ui.btn_pred_analysis_multi_next_3, 2354 ] 2355 gui_elements_to_hide = [ 2356 self._view.ui.btn_pred_analysis_multi_remove, 2357 self._view.ui.btn_pred_analysis_multi_add, 2358 self._view.ui.box_pred_analysis_multi_prot_struct_1, 2359 self._view.ui.box_pred_analysis_multi_prot_struct_2, 2360 self._view.ui.btn_pred_analysis_multi_back_3, 2361 self._view.ui.btn_pred_analysis_multi_next_2, 2362 self._view.ui.lbl_pred_analysis_multi_model_chains, 2363 self._view.ui.list_pred_analysis_multi_model_chains, 2364 self._view.ui.btn_pred_analysis_multi_back_5, 2365 self._view.ui.btn_pred_analysis_multi_next_4, 2366 self._view.ui.lbl_pred_analysis_multi_images, 2367 self._view.ui.cb_pred_analysis_multi_images, 2368 self._view.ui.btn_pred_analysis_multi_start, 2369 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 2370 ] 2371 gui_utils.show_gui_elements(gui_elements_to_show) 2372 gui_utils.hide_gui_elements(gui_elements_to_hide) 2373 self._view.ui.lbl_pred_analysis_multi_prot_struct_1.setText( 2374 self._view.ui.box_pred_analysis_multi_prot_struct_1.currentText(), 2375 ) 2376 self._view.ui.lbl_pred_analysis_multi_prot_struct_2.setText( 2377 self._view.ui.box_pred_analysis_multi_prot_struct_2.currentText(), 2378 ) 2379 self._view.ui.list_pred_analysis_multi_ref_chains.clear() 2380 self._view.ui.btn_pred_analysis_multi_next_3.setEnabled(False) 2381 self._view.ui.list_pred_analysis_multi_ref_chains.setEnabled(True) 2382 2383 for i in range(self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount()): 2384 if ( 2385 self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem(i).text() 2386 == self._view.ui.box_pred_analysis_multi_prot_struct_1.currentText() 2387 ): 2388 self._view.ui.list_pred_analysis_multi_ref_chains.addItem( 2389 self._view.ui.table_pred_analysis_multi_prot_to_predict.item(i, 0).text(), 2390 ) 2391 if self._view.ui.list_pred_analysis_multi_ref_chains.count() == 0: 2392 tmp_protein = self._current_project.search_protein( 2393 self._view.ui.box_pred_analysis_multi_prot_struct_1.currentText(), 2394 ) 2395 for tmp_chain in tmp_protein.chains: 2396 if tmp_chain.chain_type == "protein_chain": 2397 self._view.ui.list_pred_analysis_multi_ref_chains.addItem(tmp_chain.chain_letter) 2398 if self._view.ui.list_pred_analysis_multi_ref_chains.count() == 1: 2399 self._view.ui.lbl_pred_analysis_multi_ref_chains.setText( 2400 f"Select chain in protein structure {self._view.ui.lbl_pred_analysis_multi_prot_struct_1.text()}.", 2401 ) 2402 else: 2403 self._view.ui.lbl_pred_analysis_multi_ref_chains.setText( 2404 f"Select chains in protein structure {self._view.ui.lbl_pred_analysis_multi_prot_struct_1.text()}.", 2405 ) 2406 self._view.wait_spinner.stop() 2407 2408 # </editor-fold> 2409 2410 # <editor-fold desc="Structure Analysis functions"> 2411 def post_analysis_process(self, an_exit_code: tuple[int, str]) -> None: 2412 """Post process after the analysis thread finished.""" 2413 constants.PYSSA_LOGGER.debug("post_analysis_process() started ...") 2414 if an_exit_code[0] == exit_codes.ERROR_DISTANCE_ANALYSIS_FAILED[0]: 2415 self.block_box_analysis.destroy(True) 2416 basic_boxes.ok( 2417 "Distance analysis", 2418 "Distance analysis failed because there was an error during the analysis!", 2419 QtWidgets.QMessageBox.Critical, 2420 ) 2421 constants.PYSSA_LOGGER.error( 2422 f"Distance analysis ended with exit code {an_exit_code[0]}: {an_exit_code[1]}", 2423 ) 2424 elif an_exit_code[0] == exit_codes.EXIT_CODE_ONE_UNKNOWN_ERROR[0]: 2425 self.block_box_analysis.destroy(True) 2426 basic_boxes.ok( 2427 "Distance analysis", 2428 "Distance analysis failed because of an unknown error!", 2429 QtWidgets.QMessageBox.Critical, 2430 ) 2431 constants.PYSSA_LOGGER.error( 2432 f"Distance analysis ended with exit code {an_exit_code[0]}: {an_exit_code[1]}", 2433 ) 2434 elif an_exit_code[0] == exit_codes.EXIT_CODE_ZERO[0]: 2435 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 2436 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 2437 self.block_box_analysis.destroy(True) 2438 basic_boxes.ok( 2439 "Structure analysis", 2440 "All structure analysis' are done. Go to results to check the new results.", 2441 QtWidgets.QMessageBox.Information, 2442 ) 2443 constants.PYSSA_LOGGER.info("All structure analysis' are done.") 2444 2445 self._project_watcher.show_valid_options(self._view.ui) 2446 self.display_view_page() 2447 self._init_batch_analysis_page() 2448 2449 def start_process_batch(self) -> None: 2450 """Sets up the worker for the analysis task.""" 2451 constants.PYSSA_LOGGER.info("Begin analysis process.") 2452 2453 tmp_raw_analysis_run_names: list = [] 2454 for row_no in range(self._view.ui.list_analysis_batch_overview.count()): 2455 tmp_raw_analysis_run_names.append(self._view.ui.list_analysis_batch_overview.item(row_no).text()) 2456 self._active_task = tasks.Task( 2457 target=main_presenter_async.run_distance_analysis, 2458 args=( 2459 tmp_raw_analysis_run_names, 2460 self._current_project, 2461 self._application_settings, 2462 self._view.ui.cb_analysis_images.isChecked(), 2463 ), 2464 post_func=self.post_analysis_process, 2465 ) 2466 self._active_task.start() 2467 2468 if not os.path.exists(constants.SCRATCH_DIR_ANALYSIS): 2469 os.mkdir(constants.SCRATCH_DIR_ANALYSIS) 2470 2471 self.block_box_analysis.exec_() 2472 self.display_view_page() 2473 2474 def structure_analysis_next(self) -> None: 2475 """Shows the gui elements to select the chains in protein 1.""" 2476 self._view.wait_spinner.start() 2477 self._active_task = tasks.Task( 2478 target=main_presenter_async.check_chains_for_analysis, 2479 args=( 2480 self._view.ui.box_analysis_batch_prot_struct_1.currentText(), 2481 self._view.ui.box_analysis_batch_prot_struct_2.currentText(), 2482 self._current_project, 2483 ), 2484 post_func=self.__await_structure_analysis_next, 2485 ) 2486 self._active_task.start() 2487 2488 def __await_structure_analysis_next(self, result: tuple) -> None: 2489 _, tmp_is_only_one_chain, tmp_analysis_run_name, tmp_protein_1, tmp_protein_2 = result 2490 2491 if tmp_is_only_one_chain: 2492 gui_elements_to_show = [ 2493 self._view.ui.btn_analysis_batch_remove, 2494 self._view.ui.btn_analysis_batch_add, 2495 self._view.ui.lbl_analysis_batch_overview, 2496 self._view.ui.list_analysis_batch_overview, 2497 self._view.ui.lbl_analysis_batch_images, 2498 self._view.ui.cb_analysis_batch_images, 2499 self._view.ui.btn_analysis_batch_start, 2500 ] 2501 gui_elements_to_hide = [ 2502 self._view.ui.box_analysis_batch_prot_struct_1, 2503 self._view.ui.box_analysis_batch_prot_struct_2, 2504 self._view.ui.lbl_analysis_batch_prot_struct_1, 2505 self._view.ui.lbl_analysis_batch_prot_struct_2, 2506 self._view.ui.lbl_analysis_batch_vs, 2507 self._view.ui.lbl_analysis_batch_ref_chains, 2508 self._view.ui.list_analysis_batch_ref_chains, 2509 self._view.ui.lbl_analysis_batch_model_chains, 2510 self._view.ui.list_analysis_batch_model_chains, 2511 self._view.ui.btn_analysis_batch_back, 2512 self._view.ui.btn_analysis_batch_next, 2513 self._view.ui.btn_analysis_batch_back_2, 2514 self._view.ui.btn_analysis_batch_next_2, 2515 self._view.ui.btn_analysis_batch_back_3, 2516 self._view.ui.btn_analysis_batch_next_3, 2517 ] 2518 gui_utils.show_gui_elements(gui_elements_to_show) 2519 gui_utils.hide_gui_elements(gui_elements_to_hide) 2520 item = QtWidgets.QListWidgetItem(tmp_analysis_run_name) 2521 self._view.ui.list_analysis_batch_overview.addItem(item) 2522 self._view.ui.btn_analysis_batch_remove.setEnabled(False) 2523 else: 2524 gui_elements_to_show = [ 2525 self._view.ui.lbl_analysis_batch_overview, 2526 self._view.ui.list_analysis_batch_overview, 2527 self._view.ui.lbl_analysis_batch_prot_struct_1, 2528 self._view.ui.lbl_analysis_batch_prot_struct_2, 2529 self._view.ui.lbl_analysis_batch_vs, 2530 self._view.ui.lbl_analysis_batch_ref_chains, 2531 self._view.ui.list_analysis_batch_ref_chains, 2532 self._view.ui.btn_analysis_batch_back_2, 2533 self._view.ui.btn_analysis_batch_next_2, 2534 ] 2535 gui_elements_to_hide = [ 2536 self._view.ui.btn_analysis_batch_remove, 2537 self._view.ui.btn_analysis_batch_add, 2538 self._view.ui.box_analysis_batch_prot_struct_1, 2539 self._view.ui.box_analysis_batch_prot_struct_2, 2540 self._view.ui.btn_analysis_batch_back, 2541 self._view.ui.btn_analysis_batch_next, 2542 self._view.ui.lbl_analysis_batch_model_chains, 2543 self._view.ui.list_analysis_batch_model_chains, 2544 self._view.ui.btn_analysis_batch_back_3, 2545 self._view.ui.btn_analysis_batch_next_3, 2546 self._view.ui.lbl_analysis_batch_images, 2547 self._view.ui.cb_analysis_batch_images, 2548 self._view.ui.btn_analysis_batch_start, 2549 ] 2550 gui_utils.show_gui_elements(gui_elements_to_show) 2551 gui_utils.hide_gui_elements(gui_elements_to_hide) 2552 self._view.ui.lbl_analysis_batch_prot_struct_1.setText( 2553 self._view.ui.box_analysis_batch_prot_struct_1.currentText(), 2554 ) 2555 self._view.ui.lbl_analysis_batch_prot_struct_2.setText( 2556 self._view.ui.box_analysis_batch_prot_struct_2.currentText(), 2557 ) 2558 self._view.ui.list_analysis_batch_ref_chains.clear() 2559 self._view.ui.btn_analysis_batch_next_2.setEnabled(False) 2560 self._view.ui.list_analysis_batch_ref_chains.setEnabled(True) 2561 2562 for tmp_chain in tmp_protein_1.chains: 2563 if tmp_chain.chain_type == "protein_chain": 2564 self._view.ui.list_analysis_batch_ref_chains.addItem(tmp_chain.chain_letter) 2565 2566 if self._view.ui.list_analysis_batch_ref_chains.count() == 1: 2567 self._view.ui.lbl_analysis_batch_ref_chains.setText( 2568 f"Select chain in protein structure {self._view.ui.lbl_analysis_batch_prot_struct_1.text()}.", 2569 ) 2570 else: 2571 self._view.ui.lbl_analysis_batch_ref_chains.setText( 2572 f"Select chains in protein structure {self._view.ui.lbl_analysis_batch_prot_struct_1.text()}.", 2573 ) 2574 self._view.wait_spinner.stop() 2575 2576 # </editor-fold> 2577 2578 # <editor-fold desc="Analysis Images"> 2579 def post_image_creation_process(self) -> None: 2580 """Post method after the image creation task is finished.""" 2581 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 2582 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 2583 self.block_box_images.destroy(True) 2584 basic_boxes.ok( 2585 "Analysis Images", 2586 "All images of all analysis' have been created. Go to results to check the new results.", 2587 QtWidgets.QMessageBox.Information, 2588 ) 2589 constants.PYSSA_LOGGER.info("All images of all analysis' have been created.") 2590 self._init_analysis_image_page() 2591 self.display_view_page() 2592 self._project_watcher.show_valid_options(self._view.ui) 2593 2594 def start_automatic_image_creation(self) -> None: 2595 """Sets up the worker for the image creation process.""" 2596 constants.PYSSA_LOGGER.info("Begin image creation process.") 2597 # self.worker_image_creation = workers.BatchImageWorkerPool( 2598 # self._view.ui.list_analysis_images_struct_analysis, self._view.ui.list_analysis_images_creation_struct_analysis, 2599 # self._view.status_bar, self._current_project) 2600 constants.PYSSA_LOGGER.info("Thread started for image creation process.") 2601 # self.threadpool.start(self.worker_image_creation) 2602 2603 # <editor-fold desc="Worker setup"> 2604 # TODO: test code below 2605 # --Begin: worker setup 2606 self.tmp_thread = QtCore.QThread() 2607 self.tmp_worker = task_workers.BatchImageWorker( 2608 self._view.ui.list_analysis_images_struct_analysis, 2609 self._view.ui.list_analysis_images_creation_struct_analysis, 2610 self._view.status_bar, 2611 self._current_project, 2612 ) 2613 self.tmp_thread = task_workers.setup_worker_for_work(self.tmp_thread, self.tmp_worker, self.display_view_page) 2614 self.tmp_worker.finished.connect(self.post_image_creation_process) 2615 self.tmp_thread.start() 2616 # --End: worker setup 2617 2618 # </editor-fold> 2619 2620 if not os.path.exists(constants.SCRATCH_DIR_ANALYSIS): 2621 os.mkdir(constants.SCRATCH_DIR_ANALYSIS) 2622 2623 self._view.ui.list_analysis_images_struct_analysis.setEnabled(False) 2624 self._view.ui.list_analysis_images_creation_struct_analysis.setEnabled(False) 2625 2626 # gui_elements_to_show = [ 2627 # self._view.ui.btn_analysis_abort, 2628 # ] 2629 # gui_elements_to_hide = [ 2630 # self._view.ui.btn_save_project, 2631 # self._view.ui.btn_edit_page, 2632 # self._view.ui.btn_view_page, 2633 # self._view.ui.btn_use_page, 2634 # self._view.ui.btn_export_project, 2635 # self._view.ui.btn_close_project, 2636 # self._view.ui.btn_batch_analysis_page, 2637 # self._view.ui.btn_image_analysis_page, 2638 # self._view.ui.btn_results_page, 2639 # self._view.ui.lbl_handle_pymol_session, 2640 # self._view.ui.btn_image_page, 2641 # self._view.ui.btn_hotspots_page, 2642 # ] 2643 # gui_utils.manage_gui_visibility(gui_elements_to_show, gui_elements_to_hide) 2644 2645 self.block_box_images.exec_() 2646 2647 # </editor-fold> 2648 2649 # <editor-fold desc="Results page functions"> 2650 def show_analysis_results_options(self) -> None: 2651 """Shows the combo box of protein pairs.""" 2652 self.results_management.show_stage_x(0) 2653 2654 def show_results_interactions(self, gui_elements_to_show: list = None, gui_elements_to_hide: list = None) -> None: 2655 """Shows the gui elements of the results page. 2656 2657 Args: 2658 gui_elements_to_show: a list of gui elements which should get displayed. 2659 gui_elements_to_hide: a list of gui elements which should get hidden. 2660 """ 2661 if gui_elements_to_hide is not None: 2662 self.results_management.show_gui_elements_stage_x( 2663 [0, 1], 2664 [], 2665 show_specific_elements=[ 2666 self._view.ui.lbl_results_analysis_options, 2667 self._view.ui.cb_results_analysis_options, 2668 ], 2669 hide_specific_elements=gui_elements_to_hide, 2670 ) 2671 else: 2672 self.results_management.show_gui_elements_stage_x( 2673 [0, 1], 2674 [], 2675 show_specific_elements=[ 2676 self._view.ui.lbl_results_analysis_options, 2677 self._view.ui.cb_results_analysis_options, 2678 ], 2679 ) 2680 2681 def load_results(self) -> None: 2682 """Sets up the worker for the result loading process.""" 2683 self._view.wait_spinner.start() 2684 if self.is_distance_plot_open: 2685 self.distance_plot_dialog.close() 2686 self.is_distance_plot_open = False 2687 self.results_name = self._view.ui.cb_results_analysis_options.currentText() 2688 if self.results_name == "": 2689 self.show_analysis_results_options() 2690 self._view.wait_spinner.stop() 2691 return 2692 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 2693 2694 self._active_task = tasks.Task( 2695 target=main_presenter_async.load_results, 2696 args=( 2697 self._current_project, 2698 self.results_name, 2699 ), 2700 post_func=self.__await_load_results, 2701 ) 2702 self._active_task.start() 2703 2704 self._view.ui.list_results_interest_regions.clear() 2705 self._view.status_bar.showMessage(f"Loading results of {self.results_name} ...") 2706 2707 def __await_load_results(self, result: tuple) -> None: 2708 _, images_type, self.current_session, tmp_rmsd, tmp_no_aligned_residues = result 2709 2710 if images_type == constants.IMAGES_ALL: 2711 gui_elements_to_show = [ 2712 self._view.ui.lbl_results_analysis_options, 2713 self._view.ui.cb_results_analysis_options, 2714 self._view.ui.lbl_results_rmsd, 2715 self._view.ui.txt_results_rmsd, 2716 self._view.ui.lbl_color_rmsd, 2717 self._view.ui.btn_color_rmsd, 2718 self._view.ui.lbl_results_aligned_residues, 2719 self._view.ui.txt_results_aligned_residues, 2720 self._view.ui.lbl_results_distance_plot, 2721 self._view.ui.btn_view_distance_plot, 2722 self._view.ui.lbl_results_distance_histogram, 2723 self._view.ui.btn_view_distance_histogram, 2724 self._view.ui.lbl_results_distance_table, 2725 self._view.ui.btn_view_distance_table, 2726 self._view.ui.lbl_results_structure_alignment, 2727 self._view.ui.btn_view_struct_alignment, 2728 self._view.ui.lbl_results_interest_regions, 2729 self._view.ui.list_results_interest_regions, 2730 self._view.ui.btn_view_interesting_region, 2731 ] 2732 gui_utils.show_gui_elements(gui_elements_to_show) 2733 for tmp_filename in os.listdir(constants.CACHE_STRUCTURE_ALN_IMAGES_INTERESTING_REGIONS_DIR): 2734 self._view.ui.list_results_interest_regions.addItem(tmp_filename) 2735 self._view.ui.list_results_interest_regions.sortItems() 2736 elif images_type == constants.IMAGES_STRUCT_ALN_ONLY: 2737 gui_elements_to_show = [ 2738 self._view.ui.lbl_results_analysis_options, 2739 self._view.ui.cb_results_analysis_options, 2740 self._view.ui.lbl_results_rmsd, 2741 self._view.ui.txt_results_rmsd, 2742 self._view.ui.lbl_color_rmsd, 2743 self._view.ui.btn_color_rmsd, 2744 self._view.ui.lbl_results_aligned_residues, 2745 self._view.ui.txt_results_aligned_residues, 2746 self._view.ui.lbl_results_distance_plot, 2747 self._view.ui.btn_view_distance_plot, 2748 self._view.ui.lbl_results_distance_histogram, 2749 self._view.ui.btn_view_distance_histogram, 2750 self._view.ui.lbl_results_distance_table, 2751 self._view.ui.btn_view_distance_table, 2752 self._view.ui.lbl_results_structure_alignment, 2753 self._view.ui.btn_view_struct_alignment, 2754 ] 2755 gui_elements_to_hide = [ 2756 self._view.ui.lbl_results_interest_regions, 2757 self._view.ui.list_results_interest_regions, 2758 self._view.ui.btn_view_interesting_region, 2759 ] 2760 gui_utils.show_gui_elements(gui_elements_to_show) 2761 gui_utils.hide_gui_elements(gui_elements_to_hide) 2762 self._view.ui.list_results_interest_regions.sortItems() 2763 elif images_type == constants.IMAGES_NONE: 2764 gui_elements_to_show = [ 2765 self._view.ui.lbl_results_analysis_options, 2766 self._view.ui.cb_results_analysis_options, 2767 self._view.ui.lbl_results_rmsd, 2768 self._view.ui.txt_results_rmsd, 2769 self._view.ui.lbl_color_rmsd, 2770 self._view.ui.btn_color_rmsd, 2771 self._view.ui.lbl_results_aligned_residues, 2772 self._view.ui.txt_results_aligned_residues, 2773 self._view.ui.lbl_results_distance_plot, 2774 self._view.ui.btn_view_distance_plot, 2775 self._view.ui.lbl_results_distance_histogram, 2776 self._view.ui.btn_view_distance_histogram, 2777 self._view.ui.lbl_results_distance_table, 2778 self._view.ui.btn_view_distance_table, 2779 ] 2780 gui_elements_to_hide = [ 2781 self._view.ui.lbl_results_structure_alignment, 2782 self._view.ui.btn_view_struct_alignment, 2783 self._view.ui.lbl_results_interest_regions, 2784 self._view.ui.list_results_interest_regions, 2785 self._view.ui.btn_view_interesting_region, 2786 ] 2787 gui_utils.show_gui_elements(gui_elements_to_show) 2788 gui_utils.hide_gui_elements(gui_elements_to_hide) 2789 else: 2790 raise ValueError("Illegal argument.") 2791 2792 self._view.ui.txt_results_rmsd.setText(str(tmp_rmsd)) 2793 self._view.ui.txt_results_aligned_residues.setText(str(tmp_no_aligned_residues)) 2794 self._view.status_bar.showMessage(f"Current workspace: {str(self._workspace_path)}") 2795 self.main_window_state.results_page.results_name = self._view.ui.cb_results_analysis_options.currentText() 2796 self._view.wait_spinner.stop() 2797 2798 def color_protein_pair_by_rmsd(self) -> None: 2799 """Colors the residues in 5 colors depending on their distance to the reference.""" 2800 self._view.wait_spinner.start() 2801 self._active_task = tasks.Task( 2802 target=main_presenter_async.color_protein_pair_by_rmsd_value, 2803 args=( 2804 self._current_project, 2805 self.results_name, 2806 ), 2807 post_func=self.__await_color_protein_pair_by_rmsd, 2808 ) 2809 self._active_task.start() 2810 self._view.status_bar.showMessage("Coloring protein pair by RMSD value ...") 2811 # hide unnecessary representations 2812 # fixme: it might be a problem to hide any representation at this point 2813 # cmd.hide("cartoon", tmp_protein_pair.protein_1.get_molecule_object()) 2814 # cmd.hide("cartoon", f"{tmp_protein_pair.protein_2.get_molecule_object()}") 2815 # cmd.hide("cartoon", f"{tmp_protein_pair.protein_2.get_molecule_object()}") 2816 2817 def __await_color_protein_pair_by_rmsd(self, result: tuple) -> None: 2818 self._view.wait_spinner.stop() 2819 2820 # </editor-fold> 2821 2822 # <editor-fold desc="Display page functions"> 2823 def display_structure_alignment(self) -> None: 2824 """Opens a window which displays the image of the structure alignment.""" 2825 png_dialog = QtWidgets.QDialog(self._view) 2826 label = QtWidgets.QLabel(self._view) 2827 pathlib.Path( 2828 f"{self._workspace_path}/{self._view.ui.lbl_current_project_name.text()}/results/{self.results_name}", 2829 ) 2830 self._view.ui.cb_results_analysis_options.currentText() 2831 pixmap = QtGui.QPixmap( 2832 f"{constants.CACHE_STRUCTURE_ALN_IMAGES_DIR}/structure_aln_{self._view.ui.cb_results_analysis_options.currentText()}", 2833 ) 2834 # TO-DO: Create setting for min. image size 2835 pixmap = pixmap.scaled(450, 450, transformMode=QtCore.Qt.SmoothTransformation) 2836 label.setPixmap(pixmap) 2837 label.setScaledContents(True) 2838 png_dialog_layout = QtWidgets.QHBoxLayout() 2839 png_dialog_layout.addWidget(label) 2840 png_dialog.setLayout(png_dialog_layout) 2841 png_dialog.setWindowTitle("Image of: structure alignment") 2842 png_dialog.show() 2843 2844 def display_distance_plot(self) -> None: 2845 """Opens a window which displays the distance plot.""" 2846 protein_pair_of_analysis = self._current_project.search_protein_pair( 2847 self._view.ui.cb_results_analysis_options.currentText(), 2848 ) 2849 2850 tmp_dialog = plot_view.PlotView(protein_pair_of_analysis, self._current_project, self._view.ui.cb_results_analysis_options.currentText()) 2851 tmp_dialog.exec_() 2852 2853 # self.distance_plot_dialog = dialog_distance_plot.DialogDistancePlot(protein_pair_of_analysis, self._current_project, 2854 # self._view.ui.cb_results_analysis_options.currentText()) 2855 # self.distance_plot_dialog.setWindowModality(Qt.WindowModal) 2856 # self.is_distance_plot_open = True 2857 # self.distance_plot_dialog.exec_() 2858 2859 def display_distance_histogram(self) -> None: 2860 """Opens a window which displays the distance histogram.""" 2861 if self.is_distance_plot_open: 2862 self.distance_plot_dialog.close() 2863 self.is_distance_plot_open = False 2864 protein_pair_of_analysis = self._current_project.search_protein_pair( 2865 self._view.ui.cb_results_analysis_options.currentText(), 2866 ) 2867 dialog = dialog_distance_histogram.DialogDistanceHistogram(protein_pair_of_analysis) 2868 dialog.exec_() 2869 2870 def display_interesting_region(self) -> None: 2871 """Displays an image of an interesting region.""" 2872 if self.is_distance_plot_open: 2873 self.distance_plot_dialog.close() 2874 self.is_distance_plot_open = False 2875 png_dialog = QtWidgets.QDialog(self._view) 2876 label = QtWidgets.QLabel(self._view) 2877 file_name = self._view.ui.list_results_interest_regions.currentItem().text() 2878 pixmap = QtGui.QPixmap(f"{constants.CACHE_STRUCTURE_ALN_IMAGES_INTERESTING_REGIONS_DIR}/{file_name}") 2879 # TODO: Create setting for min. image size 2880 pixmap = pixmap.scaled(450, 450, transformMode=QtCore.Qt.SmoothTransformation) 2881 label.setPixmap(pixmap) 2882 label.setScaledContents(True) 2883 png_dialog_layout = QtWidgets.QHBoxLayout() 2884 png_dialog_layout.addWidget(label) 2885 png_dialog.setLayout(png_dialog_layout) 2886 png_dialog.setWindowTitle(f"Image of: {file_name}") 2887 png_dialog.show() 2888 2889 def display_distance_table(self) -> None: 2890 """Displays the distances in a table.""" 2891 if self.is_distance_plot_open: 2892 self.distance_plot_dialog.close() 2893 self.is_distance_plot_open = False 2894 csv_model = QtGui.QStandardItemModel() 2895 csv_model.setColumnCount(7) 2896 labels = [ 2897 "Residue pair no.", 2898 "Protein 1 Chain", 2899 "Protein 1 Position", 2900 "Protein 1 Residue", 2901 "Protein 2 Chain", 2902 "Protein 2 Position", 2903 "Protein 2 Residue", 2904 "Distance in Å", 2905 ] 2906 csv_model.setHorizontalHeaderLabels(labels) 2907 table_dialog = QtWidgets.QDialog(self._view) 2908 table_view = QtWidgets.QTableView() 2909 table_view.setModel(csv_model) 2910 2911 tmp_protein_pair = self._current_project.search_protein_pair( 2912 self._view.ui.cb_results_analysis_options.currentText(), 2913 ) 2914 csv_filepath = pathlib.Path(f"{constants.CACHE_CSV_DIR}/{tmp_protein_pair.name}.csv") 2915 if not os.path.exists(constants.CACHE_CSV_DIR): 2916 os.mkdir(constants.CACHE_CSV_DIR) 2917 tmp_protein_pair = self._current_project.search_protein_pair(self.results_name) 2918 2919 distance_data = tmp_protein_pair.distance_analysis.analysis_results.distance_data 2920 distance_data_array = np.array( 2921 [ 2922 distance_data[pyssa_keys.ARRAY_DISTANCE_INDEX], 2923 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_1_CHAIN], 2924 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_1_POSITION], 2925 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_1_RESI], 2926 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_2_CHAIN], 2927 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_2_POSITION], 2928 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_2_RESI], 2929 distance_data[pyssa_keys.ARRAY_DISTANCE_DISTANCES], 2930 ], 2931 ) 2932 distance_data_array_transpose = distance_data_array.transpose() 2933 with open(csv_filepath, mode="w", newline="") as file: 2934 writer = csv.writer(file, delimiter=",") 2935 writer.writerows(distance_data_array_transpose) 2936 2937 file.close() 2938 2939 with open(csv_filepath, "r", encoding="utf-8") as csv_file: 2940 i = 0 2941 for line in csv_file: 2942 tmp_list = line.split(",") 2943 # tmp_list.pop(0) 2944 standard_item_list = [] 2945 pair_no_item = QtGui.QStandardItem() 2946 pair_no_item.setData(int(tmp_list[0]), role=QtCore.Qt.DisplayRole) 2947 ref_chain_item = QtGui.QStandardItem() 2948 ref_chain_item.setData(str(tmp_list[1]), role=QtCore.Qt.DisplayRole) 2949 ref_pos_item = QtGui.QStandardItem() 2950 ref_pos_item.setData(int(tmp_list[2]), role=QtCore.Qt.DisplayRole) 2951 ref_resi_item = QtGui.QStandardItem() 2952 ref_resi_item.setData(str(tmp_list[3]), role=QtCore.Qt.DisplayRole) 2953 model_chain_item = QtGui.QStandardItem() 2954 model_chain_item.setData(str(tmp_list[4]), role=QtCore.Qt.DisplayRole) 2955 model_pos_item = QtGui.QStandardItem() 2956 model_pos_item.setData(int(tmp_list[5]), role=QtCore.Qt.DisplayRole) 2957 model_resi_item = QtGui.QStandardItem() 2958 model_resi_item.setData(str(tmp_list[6]), role=QtCore.Qt.DisplayRole) 2959 distance_item = QtGui.QStandardItem() 2960 distance_item.setData(float(tmp_list[7]), role=QtCore.Qt.DisplayRole) 2961 standard_item_list.append(pair_no_item) 2962 standard_item_list.append(ref_chain_item) 2963 standard_item_list.append(ref_pos_item) 2964 standard_item_list.append(ref_resi_item) 2965 standard_item_list.append(model_chain_item) 2966 standard_item_list.append(model_pos_item) 2967 standard_item_list.append(model_resi_item) 2968 standard_item_list.append(distance_item) 2969 csv_model.insertRow(i, standard_item_list) 2970 i += 1 2971 csv_file.close() 2972 csv_model.removeRow(0) 2973 table_view.setAlternatingRowColors(True) 2974 table_view.resizeColumnsToContents() 2975 table_view.verticalHeader().setVisible(False) 2976 table_view.setSortingEnabled(True) 2977 table_view.sortByColumn(0, QtCore.Qt.AscendingOrder) 2978 table_dialog_layout = QtWidgets.QHBoxLayout() 2979 table_dialog_layout.addWidget(table_view) 2980 table_dialog.setLayout(table_dialog_layout) 2981 # styles 2982 stylesheet = """ 2983 QDialog {background-color: #F6F4F8;} 2984 QTableView {background-color: white;} 2985 """ 2986 table_dialog.setStyleSheet(stylesheet) 2987 table_dialog.setWindowFlag(QtCore.Qt.WindowMaximizeButtonHint, True) 2988 table_dialog.setWindowFlag(QtCore.Qt.WindowCloseButtonHint, True) 2989 table_dialog.setModal(True) 2990 table_view.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers) # disables editing of cells 2991 table_dialog.setWindowTitle("Distances of Structure Alignment") 2992 table_dialog.show() 2993 2994 # </editor-fold> 2995 2996 # <editor-fold desc="Manage page functions"> 2997 def choose_manage_open_protein(self) -> None: 2998 """Shows the different configuration gui elements.""" 2999 if self._view.ui.box_manage_choose_protein.currentText() != "": 3000 gui_elements_to_show = [ 3001 self._view.ui.lbl_manage_choose_color, 3002 self._view.ui.box_manage_choose_color, 3003 self._view.ui.lbl_manage_choose_representation, 3004 self._view.ui.box_manage_choose_representation, 3005 self._view.ui.lbl_manage_choose_bg_color, 3006 self._view.ui.box_manage_choose_bg_color, 3007 ] 3008 gui_utils.show_gui_elements(gui_elements_to_show) 3009 tmp_pymol_selection_option: str = "byres (resn CYS and name SG) within 2 of (resn CYS and name SG)" 3010 if ( 3011 cmd.select( 3012 name="disulfides", 3013 selection=f"{self._view.ui.box_manage_choose_protein.currentText()} & {tmp_pymol_selection_option}", 3014 ) 3015 > 0 3016 ): 3017 gui_elements_to_show = [ 3018 self._view.ui.lbl_disulfid_bond_1, 3019 self._view.ui.lbl_disulfid_bond_2, 3020 self._view.ui.btn_disulfid_bond_show, 3021 self._view.ui.btn_disulfid_bond_hide, 3022 ] 3023 gui_utils.show_gui_elements(gui_elements_to_show) 3024 else: 3025 gui_elements_to_hide = [ 3026 self._view.ui.lbl_manage_choose_color, 3027 self._view.ui.box_manage_choose_color, 3028 self._view.ui.lbl_manage_choose_representation, 3029 self._view.ui.box_manage_choose_representation, 3030 self._view.ui.lbl_manage_choose_bg_color, 3031 self._view.ui.box_manage_choose_bg_color, 3032 self._view.ui.lbl_disulfid_bond_1, 3033 self._view.ui.lbl_disulfid_bond_2, 3034 self._view.ui.btn_disulfid_bond_show, 3035 self._view.ui.btn_disulfid_bond_hide, 3036 ] 3037 gui_utils.hide_gui_elements(gui_elements_to_hide) 3038 3039 def choose_manage_color_selected_protein(self) -> None: 3040 """Sets the protein color.""" 3041 tmp_input = self._view.ui.box_manage_choose_protein.currentText() 3042 tmp_protein = self._current_project.search_protein(tmp_input) 3043 tmp_protein.color_protein_in_pymol( 3044 self._view.ui.box_manage_choose_color.currentText(), 3045 f"/{tmp_protein.get_molecule_object()}", 3046 ) 3047 3048 def choose_manage_representation(self) -> None: 3049 """Sets the representation.""" 3050 tmp_input = self._view.ui.box_manage_choose_protein.currentText() 3051 tmp_protein = self._current_project.search_protein(tmp_input) 3052 tmp_selection = f"/{tmp_protein.get_molecule_object()}" 3053 if self._view.ui.box_manage_choose_representation.currentIndex() == 0: 3054 print("Please select a representation.") 3055 self._view.status_bar.showMessage("Please select a representation.") 3056 elif self._view.ui.box_manage_choose_representation.currentIndex() == 1: 3057 cmd.show("cartoon", tmp_selection) 3058 cmd.hide("ribbon", tmp_selection) 3059 elif self._view.ui.box_manage_choose_representation.currentIndex() == 2: 3060 cmd.show("ribbon", tmp_selection) 3061 cmd.hide("cartoon", tmp_selection) 3062 else: 3063 print("Missing implementation!") 3064 3065 def choose_manage_bg_color(self) -> None: 3066 """Sets the background color.""" 3067 if self._view.ui.box_manage_choose_bg_color.currentIndex() == 0: 3068 print("Please select a background color.") 3069 self._view.status_bar.showMessage("Please select a background color.") 3070 elif self._view.ui.box_manage_choose_bg_color.currentIndex() == 1: 3071 cmd.bg_color("black") 3072 elif self._view.ui.box_manage_choose_bg_color.currentIndex() == 2: 3073 cmd.bg_color("white") 3074 else: 3075 print("Missing implementation!") 3076 3077 def show_disulfid_bonds_as_sticks(self) -> None: 3078 """Shows all disulfid bonds within the pymol session.""" 3079 tmp_pymol_selection_option: str = "byres (resn CYS and name SG) within 2 of (resn CYS and name SG)" 3080 cmd.select( 3081 name="disulfides", 3082 selection=f"{self._view.ui.box_manage_choose_protein.currentText()} & {tmp_pymol_selection_option}", 3083 ) 3084 cmd.color(color="atomic", selection="disulfides and not elem C") 3085 cmd.set("valence", 0) # this needs to be better implemented 3086 cmd.show("sticks", "disulfides") 3087 cmd.hide("sticks", "elem H") 3088 3089 def hide_disulfid_bonds_as_sticks(self) -> None: 3090 """Hides all disulfid bonds within the pymol session.""" 3091 tmp_pymol_selection_option: str = "byres (resn CYS and name SG) within 2 of (resn CYS and name SG)" 3092 cmd.select( 3093 name="disulfides", 3094 selection=f"{self._view.ui.box_manage_choose_protein.currentText()} & {tmp_pymol_selection_option}", 3095 ) 3096 cmd.hide("sticks", "disulfides") 3097 3098 # </editor-fold> 3099 3100 # <editor-fold desc="Image page functions"> 3101 def show_representation(self) -> None: 3102 """Sets the representation.""" 3103 if self._view.ui.box_representation.currentIndex() == 0: 3104 self.main_window_state.image_page.representation = "" 3105 self._view.status_bar.showMessage("Please select a representation.") 3106 elif self._view.ui.box_representation.currentIndex() == 1: 3107 cmd.show("cartoon", "all") 3108 cmd.hide("ribbon", "all") 3109 self.main_window_state.image_page.representation = "cartoon" 3110 elif self._view.ui.box_representation.currentIndex() == 2: 3111 cmd.show("ribbon", "all") 3112 cmd.hide("cartoon", "all") 3113 self.main_window_state.image_page.representation = "ribbon" 3114 else: 3115 print("Missing implementation!") 3116 3117 def choose_bg_color(self) -> None: 3118 """Sets the background color.""" 3119 if self._view.ui.box_bg_color.currentIndex() == 0: 3120 self.main_window_state.image_page.background_color = "" 3121 self._view.status_bar.showMessage("Please select a background color.") 3122 elif self._view.ui.box_bg_color.currentIndex() == 1: 3123 cmd.bg_color("black") 3124 self.main_window_state.image_page.background_color = "black" 3125 elif self._view.ui.box_bg_color.currentIndex() == 2: 3126 cmd.bg_color("white") 3127 self.main_window_state.image_page.background_color = "white" 3128 else: 3129 print("Missing implementation!") 3130 3131 def choose_renderer(self) -> None: 3132 """Sets the renderer.""" 3133 if self._view.ui.box_renderer.currentIndex() == 0: 3134 self._view.status_bar.showMessage("Please select a renderer.") 3135 self._view.ui.cb_ray_tracing.hide() 3136 self._view.ui.label_26.hide() 3137 elif self._view.ui.box_renderer.currentIndex() == 1: 3138 self.renderer = "-1" 3139 self._view.ui.cb_ray_tracing.show() 3140 self._view.ui.label_26.show() 3141 elif self._view.ui.box_renderer.currentIndex() == 2: 3142 self.renderer = "0" 3143 self._view.ui.cb_ray_tracing.show() 3144 self._view.ui.label_26.show() 3145 else: 3146 print("Missing implementation!") 3147 self.main_window_state.image_page.renderer = self._view.ui.box_renderer.currentIndex() 3148 3149 def choose_ray_trace_mode(self) -> None: 3150 """Sets the ray-trace mode.""" 3151 if self._view.ui.box_ray_trace_mode.currentIndex() == 0: 3152 self._view.status_bar.showMessage("Please select a Ray-Trace-Mode.") 3153 elif self._view.ui.box_ray_trace_mode.currentIndex() == 1: 3154 cmd.set("ray_trace_mode", 0) 3155 elif self._view.ui.box_ray_trace_mode.currentIndex() == 2: 3156 cmd.set("ray_trace_mode", 1) 3157 elif self._view.ui.box_ray_trace_mode.currentIndex() == 3: 3158 cmd.set("ray_trace_mode", 2) 3159 elif self._view.ui.box_ray_trace_mode.currentIndex() == 4: 3160 cmd.set("ray_trace_mode", 3) 3161 else: 3162 print("Missing implementation!") 3163 self.main_window_state.image_page.ray_trace_mode = self._view.ui.box_ray_trace_mode.currentIndex() 3164 3165 def choose_ray_texture(self) -> None: 3166 """Sets the ray texture.""" 3167 if self._view.ui.box_ray_texture.currentIndex() == 0: 3168 print("Please select a Ray Texture.") 3169 self._view.status_bar.showMessage("Please select a Ray Texture.") 3170 elif self._view.ui.box_ray_texture.currentIndex() == 1: 3171 cmd.set("ray_texture", 0) 3172 elif self._view.ui.box_ray_texture.currentIndex() == 2: 3173 cmd.set("ray_texture", 1) 3174 elif self._view.ui.box_ray_texture.currentIndex() == 3: 3175 cmd.set("ray_texture", 2) 3176 elif self._view.ui.box_ray_texture.currentIndex() == 4: 3177 cmd.set("ray_texture", 3) 3178 elif self._view.ui.box_ray_texture.currentIndex() == 5: 3179 cmd.set("ray_texture", 4) 3180 elif self._view.ui.box_ray_texture.currentIndex() == 6: 3181 cmd.set("ray_texture", 5) 3182 else: 3183 print("Missing implementation!") 3184 self.main_window_state.image_page.ray_texture = self._view.ui.box_ray_texture.currentIndex() 3185 3186 def decide_ray_tracing(self) -> None: 3187 """Sets the ray-tracing options.""" 3188 print(self._view.ui.cb_ray_tracing.isChecked()) 3189 if self._view.ui.cb_ray_tracing.isChecked(): 3190 self._view.ui.cb_transparent_bg.hide() 3191 self._view.ui.label_23.hide() 3192 self._view.ui.box_renderer.setEnabled(False) 3193 self._view.ui.label_10.show() 3194 self._view.ui.box_ray_trace_mode.show() 3195 self._view.ui.label_14.show() 3196 self._view.ui.box_ray_texture.show() 3197 cmd.set("ray_opaque_background", "off") 3198 else: 3199 self._view.ui.cb_transparent_bg.show() 3200 self._view.ui.label_23.show() 3201 self._view.ui.box_renderer.setEnabled(True) 3202 self._view.ui.label_10.hide() 3203 self._view.ui.box_ray_trace_mode.hide() 3204 self._view.ui.label_14.hide() 3205 self._view.ui.box_ray_texture.hide() 3206 self.main_window_state.image_page.ray_tracing = self._view.ui.cb_ray_tracing.isChecked() 3207 3208 def decide_transparent_bg(self) -> None: 3209 """Sets the transparent background.""" 3210 if self._view.ui.cb_transparent_bg.isChecked(): 3211 cmd.set("opaque_background", "off") 3212 else: 3213 cmd.set("opaque_background", "on") 3214 self.main_window_state.image_page.transparent_background = self._view.ui.cb_transparent_bg.isChecked() 3215 3216 @staticmethod 3217 def update_scene() -> None: 3218 """Updates the current selected PyMOL scene.""" 3219 cmd.scene(key="auto", action="update") 3220 3221 def save_scene(self) -> None: 3222 """Saves the current view as a new PyMOL scene.""" 3223 # returns tuple with (name, bool) 3224 scene_name = QtWidgets.QInputDialog.getText(self._view, "Save Scene", "Enter scene name:") 3225 if scene_name[1]: 3226 cmd.scene(key=scene_name[0], action="append") 3227 3228 def post_preview_image(self) -> None: 3229 """Hides the block box of the preview process.""" 3230 self.block_box_uni.hide() 3231 self.block_box_uni.destroy(True) 3232 self._view.status_bar.showMessage("Finished preview of ray-traced image.") 3233 QtWidgets.QApplication.restoreOverrideCursor() 3234 3235 def preview_image(self) -> None: 3236 """Previews the image.""" 3237 QtWidgets.QApplication.setOverrideCursor(Qt.WaitCursor) 3238 if self._view.ui.cb_ray_tracing.isChecked(): 3239 self._view.status_bar.showMessage("Preview ray-traced image ...") 3240 # <editor-fold desc="Worker setup"> 3241 # --Begin: worker setup 3242 self.tmp_thread = QtCore.QThread() 3243 self.tmp_worker = task_workers.PreviewRayImageWorker(self.renderer) 3244 self.tmp_thread = task_workers.setup_worker_for_work( 3245 self.tmp_thread, 3246 self.tmp_worker, 3247 self.display_view_page, 3248 ) 3249 self.tmp_worker.finished.connect(self.post_preview_image) 3250 self.tmp_thread.start() 3251 # --End: worker setup 3252 3253 # </editor-fold> 3254 gui_utils.setup_standard_block_box( 3255 self.block_box_uni, 3256 "Preview ray-trace image", 3257 "Creating preview for the ray-traced image ...", 3258 ) 3259 self.block_box_uni.exec_() 3260 else: 3261 self._view.status_bar.showMessage("Preview draw image ...") 3262 cmd.draw(2400, 2400) 3263 self._view.status_bar.showMessage("Finished preview of drawn image.") 3264 QtWidgets.QApplication.restoreOverrideCursor() 3265 3266 def post_save_image(self) -> None: 3267 """Displays a message box which informs that the process has finished.""" 3268 self.block_box_uni.hide() 3269 self.block_box_uni.destroy(True) 3270 self._view.status_bar.showMessage("Finished image creation.") 3271 QtWidgets.QApplication.restoreOverrideCursor() 3272 basic_boxes.ok("Finished image creation", "The image has been created.", QtWidgets.QMessageBox.Information) 3273 3274 def save_image(self) -> None: 3275 """Saves the image as a png file.""" 3276 QtWidgets.QApplication.setOverrideCursor(Qt.WaitCursor) 3277 if self._view.ui.cb_ray_tracing.isChecked(): 3278 save_dialog = QtWidgets.QFileDialog() 3279 try: 3280 full_file_name = save_dialog.getSaveFileName(caption="Save Image", filter="Image (*.png)") 3281 if full_file_name == ("", ""): 3282 tools.quick_log_and_display( 3283 "info", 3284 "No file has been selected.", 3285 self._view.status_bar, 3286 "No file has been selected.", 3287 ) 3288 return 3289 self._view.status_bar.showMessage("Creating ray-traced image ...") 3290 3291 # <editor-fold desc="Worker setup"> 3292 # --Begin: worker setup 3293 self.tmp_thread = QtCore.QThread() 3294 self.tmp_worker = task_workers.SaveRayImageWorker(self.renderer, full_file_name[0]) 3295 self.tmp_thread = task_workers.setup_worker_for_work( 3296 self.tmp_thread, 3297 self.tmp_worker, 3298 self.display_view_page, 3299 ) 3300 self.tmp_worker.finished.connect(self.post_save_image) 3301 self.tmp_thread.start() 3302 # --End: worker setup 3303 3304 # </editor-fold> 3305 gui_utils.setup_standard_block_box( 3306 self.block_box_uni, 3307 "Save ray-trace image", 3308 "Creating the ray-traced image ...", 3309 ) 3310 self.block_box_uni.exec_() 3311 3312 # cmd.ray(2400, 2400, renderer=int(self.renderer)) 3313 # cmd.png(full_file_name[0], dpi=300) 3314 3315 except FileExistsError: 3316 tools.quick_log_and_display( 3317 "error", 3318 "File exists already.", 3319 self._view.status_bar, 3320 "File exists already.", 3321 ) 3322 except pymol.CmdException: 3323 tools.quick_log_and_display( 3324 "error", 3325 "Unexpected Error from PyMOL while saving the " "an image", 3326 self._view.status_bar, 3327 "Unexpected Error from PyMOL", 3328 ) 3329 else: 3330 save_dialog = QtWidgets.QFileDialog() 3331 try: 3332 full_file_name = save_dialog.getSaveFileName(caption="Save Image", filter="Image (*.png)") 3333 if full_file_name == ("", ""): 3334 tools.quick_log_and_display( 3335 "info", 3336 "No file has been selected.", 3337 self._view.status_bar, 3338 "No file has been selected.", 3339 ) 3340 return 3341 self._view.status_bar.showMessage("Creating draw image ...") 3342 cmd.draw(2400, 2400) 3343 cmd.png(full_file_name[0], dpi=300) 3344 self._view.status_bar.showMessage("Finished image creation.") 3345 basic_boxes.ok( 3346 "Finished image creation", 3347 "The image has been created.", 3348 QtWidgets.QMessageBox.Information, 3349 ) 3350 except FileExistsError: 3351 tools.quick_log_and_display( 3352 "error", 3353 "File exists already.", 3354 self._view.status_bar, 3355 "File exists already.", 3356 ) 3357 except pymol.CmdException: 3358 tools.quick_log_and_display( 3359 "error", 3360 "Unexpected Error from PyMOL while saving the " "an image", 3361 self._view.status_bar, 3362 "Unexpected Error from PyMOL", 3363 ) 3364 finally: 3365 QtWidgets.QApplication.restoreOverrideCursor() 3366 3367 # </editor-fold> 3368 3369 # <editor-fold desc="Hotspots page functions"> 3370 def open_protein_for_hotspots(self) -> None: 3371 """Loads the selected protein's pymol session.""" 3372 self._view.wait_spinner.start() 3373 try: 3374 tmp_name = self._view.ui.list_hotspots_choose_protein.currentItem().text() 3375 except AttributeError: 3376 self._view.wait_spinner.stop() 3377 return 3378 if self._view.ui.list_hotspots_choose_protein.currentItem().text() != "": 3379 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 3380 self._active_task = tasks.Task( 3381 target=main_presenter_async.open_protein_for_hotspots, 3382 args=( 3383 tmp_name, 3384 self._current_project, 3385 self.current_session, 3386 ), 3387 post_func=self.__await_open_protein_for_hotspots, 3388 ) 3389 self._active_task.start() 3390 self.update_status("Loading PyMOL session ...") 3391 else: 3392 self._view.wait_spinner.stop() 3393 self.update_status(self._workspace_status) 3394 3395 def __await_open_protein_for_hotspots(self, result: tuple) -> None: 3396 _, is_protein, is_protein_pair, self.current_session = result 3397 if is_protein and not is_protein_pair: 3398 gui_elements_to_show = [ 3399 self._view.ui.lbl_hotspots_resi_show, 3400 self._view.ui.btn_hotspots_resi_show, 3401 self._view.ui.lbl_hotspots_resi_hide, 3402 self._view.ui.btn_hotspots_resi_hide, 3403 self._view.ui.lbl_hotspots_resi_zoom, 3404 self._view.ui.btn_hotspots_resi_zoom, 3405 self._view.ui.btn_manage_session, 3406 ] 3407 gui_utils.show_gui_elements(gui_elements_to_show) 3408 elif is_protein_pair and not is_protein: 3409 gui_elements_to_show = [ 3410 self._view.ui.lbl_hotspots_resi_show, 3411 self._view.ui.btn_hotspots_resi_show, 3412 self._view.ui.lbl_hotspots_resi_hide, 3413 self._view.ui.btn_hotspots_resi_hide, 3414 self._view.ui.lbl_hotspots_resi_zoom, 3415 self._view.ui.btn_hotspots_resi_zoom, 3416 self._view.ui.btn_manage_session, 3417 ] 3418 gui_utils.show_gui_elements(gui_elements_to_show) 3419 else: 3420 pass 3421 self._view.wait_spinner.stop() 3422 self.update_status(self._workspace_status) 3423 3424 @staticmethod 3425 def hide_resi_sticks() -> None: 3426 """Hides the balls and sticks representation of the pymol selection.""" 3427 session_util.check_if_sele_is_empty() 3428 cmd.hide(representation="sticks", selection="sele") 3429 3430 @staticmethod 3431 def show_resi_sticks() -> None: 3432 """Shows the pymol selection as sticks.""" 3433 session_util.check_if_sele_is_empty() 3434 cmd.show(representation="sticks", selection="sele and not hydrogens") 3435 cmd.select(name="sele", selection="sele and not hydrogens") 3436 cmd.color(color="atomic", selection="sele and not elem C") 3437 cmd.set("valence", 0) # this needs to be better implemented 3438 3439 @staticmethod 3440 def zoom_resi_position() -> None: 3441 """Zooms to the pymol selection.""" 3442 session_util.check_if_sele_is_empty() 3443 cmd.zoom(selection="sele", buffer=8.0, state=0, complete=0) 3444 3445 # </editor-fold> 3446 3447 # </editor-fold> 3448 3449 # <editor-fold desc="GUI related methods"> 3450 3451 # <editor-fold desc="GUI page management functions"> 3452 def _create_batch_analysis_management(self) -> None: 3453 """Creates a list of gui stages.""" 3454 # gui element management 3455 tmp_stages = [ 3456 # add a prot analysis: stage 0 3457 stage.Stage( 3458 { 3459 "label_batch_analysis_overview": self._view.ui.lbl_analysis_batch_overview, 3460 "box_protein_structure_1": self._view.ui.list_analysis_batch_overview, 3461 }, 3462 { 3463 "add_button": self._view.ui.btn_analysis_batch_add, 3464 "remove_button": self._view.ui.btn_analysis_batch_remove, 3465 }, 3466 ), 3467 # choose protein structures: stage 1 3468 stage.Stage( 3469 { 3470 "label_protein_structure_1": self._view.ui.lbl_analysis_batch_prot_struct_1, 3471 "box_protein_structure_1": self._view.ui.box_analysis_batch_prot_struct_1, 3472 "label_vs": self._view.ui.lbl_analysis_batch_vs, 3473 "label_protein_structure_2": self._view.ui.lbl_analysis_batch_prot_struct_2, 3474 "box_protein_structure_2": self._view.ui.box_analysis_batch_prot_struct_2, 3475 }, 3476 { 3477 "next_button": self._view.ui.btn_analysis_batch_next, 3478 "back_button": self._view.ui.btn_analysis_batch_back, 3479 }, 3480 ), 3481 # choose chains from prot structure 1: stage 2 3482 stage.Stage( 3483 { 3484 "label_protein_structure_1_chains": self._view.ui.lbl_analysis_batch_ref_chains, 3485 "list_protein_structure_1_chains": self._view.ui.list_analysis_batch_ref_chains, 3486 }, 3487 { 3488 "back_button": self._view.ui.btn_analysis_batch_back_2, 3489 "next_button": self._view.ui.btn_analysis_batch_next_2, 3490 }, 3491 ), 3492 # choose chains from prot structure 2: stage 3 3493 stage.Stage( 3494 { 3495 "label_protein_structure_2_chains": self._view.ui.lbl_analysis_batch_model_chains, 3496 "list_protein_structure_2_chains": self._view.ui.list_analysis_batch_model_chains, 3497 }, 3498 { 3499 "back_button": self._view.ui.btn_analysis_batch_back_3, 3500 "next_button": self._view.ui.btn_analysis_batch_next_3, 3501 }, 3502 ), 3503 # start batch run: stage 4 3504 stage.Stage( 3505 { 3506 "label_images": self._view.ui.lbl_analysis_batch_images, 3507 "checkbox_images": self._view.ui.cb_analysis_batch_images, 3508 }, 3509 { 3510 "start_button": self._view.ui.btn_analysis_batch_start, 3511 }, 3512 ), 3513 ] 3514 self.batch_analysis_management = gui_page_management.GuiPageManagement(tmp_stages) 3515 3516 def _create_results_management(self) -> None: 3517 """Creates a list of gui stages.""" 3518 # gui element management 3519 tmp_stages = [ 3520 # choose protein structures: stage 0 3521 stage.Stage( 3522 { 3523 "label_analysis_options": self._view.ui.lbl_results_analysis_options, 3524 "box_results_analysis_options": self._view.ui.cb_results_analysis_options, 3525 }, 3526 { 3527 "": None, 3528 }, 3529 ), 3530 # choose chains from prot structure 1: stage 1 3531 stage.Stage( 3532 { 3533 "label_results_rmsd": self._view.ui.lbl_results_rmsd, 3534 "text_results_rmsd": self._view.ui.txt_results_rmsd, 3535 "label_color_rmsd": self._view.ui.lbl_color_rmsd, 3536 "button_color_rmsd": self._view.ui.btn_color_rmsd, 3537 "label_results_aligned_residues": self._view.ui.lbl_results_aligned_residues, 3538 "text_results_aligned_residues": self._view.ui.txt_results_aligned_residues, 3539 "label_results_distance_plot": self._view.ui.lbl_results_distance_plot, 3540 "button_view_distance_plot": self._view.ui.btn_view_distance_plot, 3541 "label_results_distance_histogram": self._view.ui.lbl_results_distance_histogram, 3542 "button_view_distance_histogram": self._view.ui.btn_view_distance_histogram, 3543 "label_results_distance_table": self._view.ui.lbl_results_distance_table, 3544 "button_view_distance_table": self._view.ui.btn_view_distance_table, 3545 "label_results_structure_alignment": self._view.ui.lbl_results_structure_alignment, 3546 "button_view_struct_alignment": self._view.ui.btn_view_struct_alignment, 3547 "label_results_interest_regions": self._view.ui.lbl_results_interest_regions, 3548 "list_results_interest_regions": self._view.ui.list_results_interest_regions, 3549 "button_results_interest_regions": self._view.ui.btn_view_interesting_region, 3550 }, 3551 { 3552 "": None, 3553 }, 3554 ), 3555 ] 3556 self.results_management = gui_page_management.GuiPageManagement(tmp_stages) 3557 3558 # </editor-fold> 3559 3560 # <editor-fold desc="Page init functions"> 3561 def _init_fill_combo_boxes(self) -> None: 3562 """Fills all combo boxes of the plugin.""" 3563 item_list_representation = [ 3564 "", 3565 "cartoon", 3566 "ribbon", 3567 ] 3568 gui_utils.fill_combo_box(self._view.ui.box_representation, item_list_representation) 3569 gui_utils.fill_combo_box(self._view.ui.box_manage_choose_representation, item_list_representation) 3570 # combo box BgColor 3571 item_list_bg_color = [ 3572 "", 3573 "black", 3574 "white", 3575 ] 3576 gui_utils.fill_combo_box(self._view.ui.box_bg_color, item_list_bg_color) 3577 gui_utils.fill_combo_box(self._view.ui.box_manage_choose_bg_color, item_list_bg_color) 3578 # combo box Renderer 3579 item_list_renderer = [ 3580 "", 3581 "default renderer", 3582 "PyMOL internal renderer", 3583 ] 3584 gui_utils.fill_combo_box(self._view.ui.box_renderer, item_list_renderer) 3585 # combo box RayTraceMode 3586 item_list_ray_trace_mode = [ 3587 "", 3588 "normal color", 3589 "normal color + black outline", 3590 "black outline only", 3591 "quantized color + black outline", 3592 ] 3593 gui_utils.fill_combo_box(self._view.ui.box_ray_trace_mode, item_list_ray_trace_mode) 3594 # combo box Ray Texture 3595 item_list_ray_texture = [ 3596 "", 3597 "None", 3598 "Matte 1", 3599 "Matte 2", 3600 "Swirl 1", 3601 "Fiber", 3602 ] 3603 gui_utils.fill_combo_box(self._view.ui.box_ray_texture, item_list_ray_texture) 3604 # combo box protein Colors 3605 gui_utils.fill_combo_box(self._view.ui.box_manage_choose_color, constants.PYMOL_COLORS) 3606 3607 def _init_new_page(self) -> None: 3608 """Clears all text fields and hides everything which is needed.""" 3609 self._view.ui.txt_new_project_name.clear() 3610 self._view.ui.txt_new_choose_reference.clear() 3611 self._view.ui.lbl_new_status_project_name.setText("") 3612 self._view.ui.lbl_new_status_choose_reference.setText("") 3613 self._view.ui.cb_new_add_reference.setCheckState(0) 3614 self._view.ui.btn_new_create_project.setEnabled(False) 3615 styles.color_button_not_ready(self._view.ui.btn_new_create_project) 3616 3617 def _init_use_page(self) -> None: 3618 """Clears all text fields and hides everything which is needed.""" 3619 gui_elements = [ 3620 self._view.ui.lbl_use_search, 3621 self._view.ui.lbl_use_status_search, 3622 self._view.ui.txt_use_search, 3623 self._view.ui.btn_use_add_available_protein_structures, 3624 self._view.ui.lbl_use_available_protein_structures, 3625 self._view.ui.list_use_available_protein_structures, 3626 self._view.ui.btn_use_remove_selected_protein_structures, 3627 self._view.ui.lbl_use_selected_protein_structures, 3628 self._view.ui.list_use_selected_protein_structures, 3629 self._view.ui.btn_use_back, 3630 self._view.ui.btn_use_create_new_project, 3631 self._view.ui.lbl_use_new_project, 3632 ] 3633 gui_utils.hide_gui_elements(gui_elements) 3634 self._view.ui.txt_use_project_name.clear() 3635 self._view.ui.lbl_use_status_project_name.setText("") 3636 self._view.ui.txt_use_search.clear() 3637 self._view.ui.lbl_use_status_search.setText("") 3638 self._view.ui.list_use_available_protein_structures.clear() 3639 self._view.ui.list_use_selected_protein_structures.clear() 3640 self._view.ui.list_use_existing_projects.clear() 3641 self._view.ui.btn_use_next.setEnabled(False) 3642 self.hide_protein_selection_for_use() 3643 3644 def _init_edit_page(self) -> None: 3645 """Clears all text fields and hides everything which is needed.""" 3646 self._view.ui.list_edit_project_proteins.clear() 3647 gui_elements_to_hide = [ 3648 self._view.ui.lbl_edit_clean_new_prot, 3649 self._view.ui.btn_edit_clean_new_prot, 3650 self._view.ui.lbl_edit_clean_update_prot, 3651 self._view.ui.btn_edit_clean_update_prot, 3652 self._view.ui.label_12, 3653 self._view.ui.btn_edit_project_delete, 3654 self._view.ui.label_15, 3655 self._view.ui.btn_edit_protein_rename, 3656 self._view.ui.btn_edit_project_save, 3657 self._view.ui.label_13, 3658 ] 3659 gui_utils.hide_gui_elements(gui_elements_to_hide) 3660 gui_utils.fill_list_view_with_protein_names(self._current_project, self._view.ui.list_edit_project_proteins) 3661 # self.project_scanner.scan_project_for_valid_proteins(self._view.ui.list_edit_project_proteins) 3662 3663 def _init_sequence_vs_pdb_page(self) -> None: 3664 """Clears all text fields and hides everything which is needed.""" 3665 self._view.ui.list_s_v_p_ref_chains.clear() 3666 # # sets up defaults: Prediction + Analysis 3667 # 3668 # #self._view.ui.label_18.hide() 3669 # #self._view.ui.txt_prediction_project_name.hide() 3670 # #self._view.ui.lbl_prediction_status_project_name.hide() 3671 # # stage 1 3672 # self._view.ui.lbl_prediction_status_project_name.setText("") 3673 # 3674 # #self._view.ui.list_widget_projects.hide() 3675 # #self._view.ui.btn_prediction_next_1.hide() 3676 # # stage 2 3677 # self._view.ui.lbl_prediction_load_reference.hide() 3678 # self._view.ui.txt_prediction_load_reference.clear() 3679 # self._view.ui.txt_prediction_load_reference.hide() 3680 # self._view.ui.lbl_prediction_status_load_reference.setText("") 3681 # self._view.ui.btn_prediction_back_2.setEnabled(False) 3682 # self._view.ui.btn_prediction_back_2.hide() 3683 # self._view.ui.btn_prediction_next_2.setEnabled(False) 3684 # self._view.ui.btn_prediction_next_2.hide() 3685 # 3686 # # stage 3 3687 # self._view.ui.lbl_prediction_ref_chains.hide() 3688 # self._view.ui.list_widget_ref_chains.hide() 3689 # # TO-DO: stylesheet needs to be integrated into the styles.css 3690 # self._view.ui.list_widget_ref_chains.setStyleSheet("border-style: solid;" 3691 # "border-width: 2px;" 3692 # "border-radius: 8px;" 3693 # "border-color: #DCDBE3;") 3694 # self._view.ui.list_widget_ref_chains.setSelectionMode(PyQt5.QtWidgets.QAbstractItemView.ExtendedSelection) 3695 # self._view.ui.btn_prediction_back_3.setEnabled(False) 3696 # self._view.ui.btn_prediction_back_3.hide() 3697 # self._view.ui.btn_prediction_start.setEnabled(False) 3698 # self._view.ui.btn_prediction_start.hide() 3699 # # TO-DO: needs to be removed if model chains are implemented at the right spot 3700 # self._view.ui.lbl_prediction_model_chains.hide() 3701 # self._view.ui.txt_prediction_chain_model.hide() 3702 3703 def _init_results_page(self) -> None: 3704 """Clears all text fields and hides everything which is needed.""" 3705 # stage 1 3706 self._view.ui.list_results_interest_regions.clear() 3707 self._view.ui.txt_results_rmsd.clear() 3708 self._view.ui.txt_results_aligned_residues.clear() 3709 3710 def _init_analysis_image_page(self) -> None: 3711 """Clears all text fields and hides everything which is needed.""" 3712 self._view.ui.list_analysis_images_struct_analysis.setEnabled(True) 3713 self._view.ui.list_analysis_images_creation_struct_analysis.setEnabled(True) 3714 self.display_image_analysis_page() 3715 3716 def _init_image_page(self) -> None: 3717 """Hides everything which is needed.""" 3718 self._view.ui.label_10.hide() 3719 self._view.ui.box_ray_trace_mode.hide() 3720 self._view.ui.label_14.hide() 3721 self._view.ui.box_ray_texture.hide() 3722 3723 def _init_batch_analysis_page(self) -> None: 3724 """Clears all text fields and hides everything which is needed.""" 3725 # sets up defaults: Batch 3726 self.batch_analysis_management.show_stage_x(0) 3727 self._view.ui.list_analysis_batch_overview.clear() 3728 self._view.ui.btn_analysis_batch_remove.hide() 3729 3730 def _init_all_pages(self) -> None: 3731 """Collection of all init methods to reset all page defaults.""" 3732 self._init_local_pred_mono_page() 3733 self._init_local_pred_multi_page() 3734 self._init_mono_pred_analysis_page() 3735 self._init_multi_pred_analysis_page() 3736 self._init_sequence_vs_pdb_page() 3737 self._init_batch_analysis_page() 3738 self._init_analysis_image_page() 3739 self._init_results_page() 3740 self._init_image_page() 3741 3742 # </editor-fold> 3743 3744 # <editor-fold desc="Display page functions"> 3745 def display_home_page(self) -> None: 3746 """Displays the homepage of the plugin.""" 3747 if self.is_distance_plot_open: 3748 self.distance_plot_dialog.close() 3749 self.is_distance_plot_open = False 3750 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 0, "Home") 3751 3752 def display_job_analysis_page(self) -> None: 3753 """Displays the job analysis work area.""" 3754 self._view.ui.list_analysis_batch_ref_chains.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection) 3755 self._view.ui.list_analysis_batch_model_chains.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection) 3756 # regular work area opening 3757 self._init_batch_analysis_page() 3758 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 4, "Structure Analysis") 3759 self.last_sidebar_button = styles.color_sidebar_buttons( 3760 self.last_sidebar_button, 3761 self._view.ui.btn_batch_analysis_page, 3762 ) 3763 3764 def display_results_page(self) -> None: 3765 """Displays the results work area.""" 3766 if self.is_distance_plot_open: 3767 self.distance_plot_dialog.close() 3768 self.is_distance_plot_open = False 3769 results = [] 3770 results.insert(0, "") 3771 3772 for tmp_protein_pair in self._current_project.protein_pairs: 3773 results.append(tmp_protein_pair.name) 3774 if tmp_protein_pair.name == self.results_name: 3775 pass 3776 self._view.ui.cb_results_analysis_options.clear() 3777 gui_utils.fill_combo_box(self._view.ui.cb_results_analysis_options, results) 3778 3779 desired_string: str = self.main_window_state.results_page.results_name 3780 # Find the index of the string in the combo box 3781 index = self._view.ui.cb_results_analysis_options.findText(desired_string) 3782 # Set the current index of the combo box 3783 if index != -1: 3784 self._view.ui.cb_results_analysis_options.setCurrentIndex(index) 3785 else: 3786 print(f"String '{desired_string}' not found in the combo box.") 3787 3788 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 5, "Results") 3789 self.last_sidebar_button = styles.color_sidebar_buttons( 3790 self.last_sidebar_button, 3791 self._view.ui.btn_results_page, 3792 ) 3793 3794 def display_image_page(self) -> None: 3795 """Displays the image work area.""" 3796 if self.is_distance_plot_open: 3797 self.distance_plot_dialog.close() 3798 self.is_distance_plot_open = False 3799 self._init_image_page() 3800 3801 if self.main_window_state.image_page.transparent_background: 3802 self._view.ui.cb_transparent_bg.setChecked(True) 3803 else: 3804 self._view.ui.cb_transparent_bg.setChecked(False) 3805 if self.main_window_state.image_page.ray_tracing: 3806 self._view.ui.cb_ray_tracing.setChecked(True) 3807 else: 3808 self._view.ui.cb_ray_tracing.setChecked(False) 3809 try: 3810 self._view.ui.box_representation.setCurrentIndex( 3811 self._view.ui.box_representation.findText(self.main_window_state.image_page.representation), 3812 ) 3813 self._view.ui.box_bg_color.setCurrentIndex( 3814 self._view.ui.box_bg_color.findText(self.main_window_state.image_page.background_color), 3815 ) 3816 self._view.ui.box_renderer.setCurrentIndex(self.main_window_state.image_page.renderer) 3817 self._view.ui.box_ray_trace_mode.setCurrentIndex(self.main_window_state.image_page.ray_trace_mode) 3818 self._view.ui.box_ray_texture.setCurrentIndex(self.main_window_state.image_page.ray_texture) 3819 except IndexError: 3820 constants.PYSSA_LOGGER.error("An option is invalid.") 3821 3822 if self._view.ui.box_renderer.currentText() == "": 3823 self._view.ui.cb_ray_tracing.hide() 3824 self._view.ui.label_26.hide() 3825 else: 3826 self._view.ui.cb_ray_tracing.show() 3827 self._view.ui.label_26.show() 3828 3829 if self._view.ui.cb_ray_tracing.isChecked(): 3830 self._view.ui.label_10.show() 3831 self._view.ui.box_ray_trace_mode.show() 3832 self._view.ui.label_14.show() 3833 self._view.ui.box_ray_texture.show() 3834 else: 3835 self._view.ui.label_10.hide() 3836 self._view.ui.box_ray_trace_mode.hide() 3837 self._view.ui.label_14.hide() 3838 self._view.ui.box_ray_texture.hide() 3839 3840 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_image_page) 3841 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 6, "Image") 3842 3843 def display_new_page(self) -> None: 3844 """Displays the new project work area.""" 3845 self._init_new_page() 3846 self._view.ui.list_new_projects.clear() 3847 # pre-process 3848 gui_elements_to_hide = [ 3849 self._view.ui.lbl_new_choose_reference, 3850 self._view.ui.txt_new_choose_reference, 3851 self._view.ui.btn_new_choose_reference, 3852 ] 3853 gui_utils.hide_gui_elements(gui_elements_to_hide) 3854 self._view.status_bar.showMessage(self._workspace_label.text()) 3855 tools.scan_workspace_for_valid_projects(self._workspace_path, self._view.ui.list_new_projects) 3856 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 7, "Create new project") 3857 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_new_page) 3858 3859 def display_open_page(self) -> None: 3860 """Displays the open project work area.""" 3861 self._view.ui.txt_open_search.clear() 3862 self._view.ui.txt_open_selected_project.clear() 3863 if safeguard.Safeguard.check_filepath(self._workspace_path): 3864 self._view.ui.list_open_projects.clear() 3865 # pre-process 3866 self._view.status_bar.showMessage(self._workspace_label.text()) 3867 try: 3868 tools.scan_workspace_for_valid_projects(self._workspace_path, self._view.ui.list_open_projects) 3869 except PermissionError: 3870 gui_utils.error_dialog_settings( 3871 "The settings file is corrupted. Please restore the settings!", 3872 "", 3873 self._application_settings, 3874 ) 3875 self.display_home_page() 3876 return 3877 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 8, "Open existing project") 3878 self.last_sidebar_button = styles.color_sidebar_buttons( 3879 self.last_sidebar_button, 3880 self._view.ui.btn_open_page, 3881 ) 3882 else: 3883 gui_utils.error_dialog_settings( 3884 "The settings file is corrupted. Please restore the settings!", 3885 "", 3886 self._application_settings, 3887 ) 3888 self.display_home_page() 3889 3890 def display_delete_page(self) -> None: 3891 """Displays the "delete" project work area.""" 3892 self._view.ui.txt_delete_search.clear() 3893 self._view.ui.txt_delete_selected_projects.clear() 3894 self._view.ui.list_delete_projects.clear() 3895 # pre-process 3896 self._view.status_bar.showMessage(self._workspace_label.text()) 3897 tools.scan_workspace_for_valid_projects(self._workspace_path, self._view.ui.list_delete_projects) 3898 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 9, "Delete existing project") 3899 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_delete_page) 3900 3901 def display_edit_page(self) -> None: 3902 """Displays the edit project page.""" 3903 if self.is_distance_plot_open: 3904 self.distance_plot_dialog.close() 3905 self.is_distance_plot_open = False 3906 # pre-process 3907 self._view.status_bar.showMessage(self._workspace_label.text()) 3908 self._init_edit_page() 3909 tools.switch_page( 3910 self._view.ui.stackedWidget, 3911 self._view.ui.lbl_page_title, 3912 13, 3913 "Edit proteins of current project", 3914 ) 3915 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_edit_page) 3916 if len(self._view.ui.list_edit_project_proteins) >= 2: 3917 self._view.ui.btn_edit_existing_protein_struct.hide() 3918 self._view.ui.lbl_edit_existing_protein_struct.hide() 3919 else: 3920 self._view.ui.btn_edit_existing_protein_struct.show() 3921 self._view.ui.lbl_edit_existing_protein_struct.show() 3922 3923 def display_hotspots_page(self) -> None: 3924 """Displays the hotspots page.""" 3925 if self.is_distance_plot_open: 3926 self.distance_plot_dialog.close() 3927 self.is_distance_plot_open = False 3928 try: 3929 print(self._view.ui.list_hotspots_choose_protein.currentItem().text()) 3930 except AttributeError: 3931 self._view.ui.list_hotspots_choose_protein.clear() 3932 gui_elements_to_hide = [ 3933 self._view.ui.lbl_hotspots_resi_no, 3934 self._view.ui.sp_hotspots_resi_no, 3935 self._view.ui.lbl_hotspots_resi_show, 3936 self._view.ui.btn_hotspots_resi_show, 3937 self._view.ui.lbl_hotspots_resi_hide, 3938 self._view.ui.btn_hotspots_resi_hide, 3939 self._view.ui.lbl_hotspots_resi_zoom, 3940 self._view.ui.btn_hotspots_resi_zoom, 3941 ] 3942 gui_utils.hide_gui_elements(gui_elements_to_hide) 3943 gui_utils.fill_list_view_with_protein_names( 3944 self._current_project, 3945 self._view.ui.list_hotspots_choose_protein, 3946 ) 3947 gui_utils.fill_list_view_with_protein_pair_names( 3948 self._current_project, 3949 self._view.ui.list_hotspots_choose_protein, 3950 ) 3951 # self.project_scanner.scan_project_for_valid_proteins(self._view.ui.list_hotspots_choose_protein) 3952 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 18, "Hotspots") 3953 self.last_sidebar_button = styles.color_sidebar_buttons( 3954 self.last_sidebar_button, 3955 self._view.ui.btn_hotspots_page, 3956 ) 3957 3958 def display_manage_pymol_session(self) -> None: 3959 """Displays the manage pymol session page.""" 3960 if self.is_distance_plot_open: 3961 self.distance_plot_dialog.close() 3962 self.is_distance_plot_open = False 3963 self._view.ui.box_manage_choose_protein.clear() 3964 pymol_objs = cmd.get_object_list() 3965 pymol_objs.insert(0, "") 3966 for tmp_object in pymol_objs: 3967 self._view.ui.box_manage_choose_protein.addItem(tmp_object) 3968 self._view.ui.box_manage_choose_protein.setCurrentIndex( 3969 self.pymol_session_specs[pyssa_keys.SESSION_SPEC_PROTEIN][0], 3970 ) 3971 self._view.ui.box_manage_choose_color.setCurrentIndex( 3972 self.pymol_session_specs[pyssa_keys.SESSION_SPEC_COLOR][0], 3973 ) 3974 self._view.ui.box_manage_choose_representation.setCurrentIndex( 3975 self.pymol_session_specs[pyssa_keys.SESSION_SPEC_REPRESENTATION][0], 3976 ) 3977 self._view.ui.box_manage_choose_bg_color.setCurrentIndex( 3978 self.pymol_session_specs[pyssa_keys.SESSION_SPEC_BG_COLOR][0], 3979 ) 3980 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 24, "Manage PyMOL session") 3981 self.last_sidebar_button = styles.color_sidebar_buttons( 3982 self.last_sidebar_button, 3983 self._view.ui.btn_manage_session, 3984 ) 3985 gui_elements_to_hide = [ 3986 self._view.ui.lbl_manage_choose_color, 3987 self._view.ui.box_manage_choose_color, 3988 self._view.ui.lbl_manage_choose_representation, 3989 self._view.ui.box_manage_choose_representation, 3990 self._view.ui.lbl_manage_choose_bg_color, 3991 self._view.ui.box_manage_choose_bg_color, 3992 self._view.ui.lbl_disulfid_bond_1, 3993 self._view.ui.lbl_disulfid_bond_2, 3994 self._view.ui.btn_disulfid_bond_show, 3995 self._view.ui.btn_disulfid_bond_hide, 3996 ] 3997 gui_utils.hide_gui_elements(gui_elements_to_hide) 3998 3999 # </editor-fold> 4000 4001 # <editor-fold desc="New project"> 4002 def show_add_reference(self) -> None: 4003 """Shows the reference input section.""" 4004 # checkbox is checked 4005 self._view.ui.cb_new_add_reference.checkState() 4006 if self._view.ui.cb_new_add_reference.checkState() == 2: 4007 self._view.ui.txt_new_choose_reference.clear() 4008 self._view.ui.txt_new_choose_reference.setStyleSheet("background-color: white") 4009 self._view.ui.lbl_new_choose_reference.show() 4010 self._view.ui.txt_new_choose_reference.show() 4011 self._view.ui.btn_new_choose_reference.show() 4012 self._view.ui.btn_new_create_project.setEnabled(False) 4013 styles.color_button_not_ready(self._view.ui.btn_new_create_project) 4014 # check internet connectivity 4015 if not tools.check_internet_connectivity(): 4016 gui_utils.no_internet_dialog() 4017 self._view.ui.txt_new_choose_reference.setEnabled(False) 4018 self._view.ui.lbl_new_status_choose_reference.setText("You cannot enter a PDB ID (no internet).") 4019 return 4020 self._view.ui.txt_new_choose_reference.setEnabled(True) 4021 self._view.ui.lbl_new_status_choose_reference.setText("") 4022 else: 4023 self._view.ui.lbl_new_choose_reference.hide() 4024 self._view.ui.txt_new_choose_reference.hide() 4025 self._view.ui.btn_new_choose_reference.hide() 4026 self._view.ui.lbl_new_status_choose_reference.setText("") 4027 self._view.ui.btn_new_create_project.setEnabled(True) 4028 4029 def load_reference_in_project(self) -> None: 4030 """Loads a reference in a new project.""" 4031 try: 4032 # open file dialog 4033 file_name = QtWidgets.QFileDialog.getOpenFileName( 4034 self._view, 4035 "Open Reference", 4036 QtCore.QDir.homePath(), 4037 "PDB Files (*.pdb)", 4038 ) 4039 if file_name == ("", ""): 4040 raise ValueError 4041 # display path in text box 4042 self._view.ui.txt_new_choose_reference.setText(str(file_name[0])) 4043 self._view.ui.txt_new_choose_reference.setEnabled(False) 4044 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #000000") 4045 self._view.ui.btn_new_create_project.setEnabled(True) 4046 except ValueError: 4047 print("No file has been selected.") 4048 4049 def validate_reference_in_project(self) -> None: 4050 """Checks if the entered reference protein is valid or not.""" 4051 if len(self._view.ui.txt_new_choose_reference.text()) == 0: 4052 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4053 self._view.ui.lbl_new_status_choose_reference.setText("") 4054 self._view.ui.btn_new_create_project.setEnabled(False) 4055 styles.color_button_not_ready(self._view.ui.btn_new_create_project) 4056 elif len(self._view.ui.txt_new_choose_reference.text()) < 4: 4057 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4058 styles.color_button_not_ready(self._view.ui.btn_new_create_project) 4059 self._view.ui.btn_new_create_project.setEnabled(False) 4060 self._view.ui.lbl_new_status_choose_reference.setText("") 4061 # checks if a pdb id was entered 4062 elif len(self._view.ui.txt_new_choose_reference.text()) == 4: 4063 pdb_id = self._view.ui.txt_new_choose_reference.text().upper() 4064 try: 4065 # the pdb file gets saved in a scratch directory where it gets deleted immediately 4066 cmd.fetch(pdb_id, type="pdb", path=constants.SCRATCH_DIR) 4067 os.remove(f"{constants.SCRATCH_DIR}/{pdb_id}.pdb") 4068 cmd.reinitialize() 4069 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #000000") 4070 self._view.ui.btn_new_create_project.setEnabled(True) 4071 # if the id does not exist an exception gets raised 4072 except pymol.CmdException: 4073 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4074 return 4075 except FileNotFoundError: 4076 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4077 self._view.ui.lbl_new_status_choose_reference.setText("Invalid PDB ID.") 4078 self._view.ui.btn_new_create_project.setEnabled(False) 4079 return 4080 else: 4081 if self._view.ui.txt_new_choose_reference.text().find("/") == -1: 4082 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4083 self._view.ui.btn_new_create_project.setEnabled(False) 4084 styles.color_button_not_ready(self._view.ui.btn_new_create_project) 4085 4086 elif self._view.ui.txt_new_choose_reference.text().find("\\") == -1: 4087 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4088 self._view.ui.btn_new_create_project.setEnabled(False) 4089 styles.color_button_not_ready(self._view.ui.btn_new_create_project) 4090 4091 def validate_project_name(self) -> None: 4092 """Validates the input of the project name in real-time.""" 4093 input_validator.InputValidator.validate_project_name( 4094 self._view.ui.list_new_projects, 4095 self._view.ui.txt_new_project_name, 4096 self._view.ui.lbl_new_status_project_name, 4097 self._view.ui.btn_new_create_project, 4098 self._view.ui.cb_new_add_reference, 4099 ) 4100 4101 # </editor-fold> 4102 4103 # <editor-fold desc="Open project"> 4104 def validate_open_search(self) -> None: 4105 """Validates the input of the project name in real-time.""" 4106 if self._view.ui.list_open_projects.currentItem() is not None: 4107 self._view.ui.list_open_projects.currentItem().setSelected(False) 4108 # set color for lineEdit 4109 input_validator.InputValidator.validate_search_input( 4110 self._view.ui.list_open_projects, 4111 self._view.ui.txt_open_search, 4112 self._view.ui.lbl_open_status_search, 4113 self._view.ui.txt_open_selected_project, 4114 ) 4115 4116 def select_project_from_open_list(self) -> None: 4117 """Sets the selected project name in the text box.""" 4118 try: 4119 self._view.ui.txt_open_selected_project.setText(self._view.ui.list_open_projects.currentItem().text()) 4120 except AttributeError: 4121 self._view.ui.txt_open_selected_project.setText("") 4122 4123 def activate_open_button(self) -> None: 4124 """Activates the open button.""" 4125 if self._view.ui.txt_open_selected_project.text() == "": 4126 self._view.ui.btn_open_open_project.setEnabled(False) 4127 else: 4128 self._view.ui.btn_open_open_project.setEnabled(True) 4129 4130 # </editor-fold> 4131 4132 # <editor-fold desc="Delete project"> 4133 def select_project_from_delete_list(self) -> None: 4134 """Selects a project from the project list on the delete page.""" 4135 try: 4136 self._view.ui.txt_delete_selected_projects.setText(self._view.ui.list_delete_projects.currentItem().text()) 4137 except AttributeError: 4138 self._view.ui.txt_delete_selected_projects.setText("") 4139 4140 def activate_delete_button(self) -> None: 4141 """Activates the delete button.""" 4142 if self._view.ui.txt_delete_selected_projects.text() == "": 4143 self._view.ui.btn_delete_delete_project.setEnabled(False) 4144 else: 4145 self._view.ui.btn_delete_delete_project.setEnabled(True) 4146 4147 def validate_delete_search(self) -> None: 4148 """Validates the input of the project name in real-time.""" 4149 if self._view.ui.list_delete_projects.currentItem() is not None: 4150 self._view.ui.list_delete_projects.currentItem().setSelected(False) 4151 # set color for lineEdit 4152 input_validator.InputValidator.validate_search_input( 4153 self._view.ui.list_delete_projects, 4154 self._view.ui.txt_delete_search, 4155 self._view.ui.lbl_delete_status_search, 4156 self._view.ui.txt_delete_selected_projects, 4157 ) 4158 4159 # </editor-fold> 4160 4161 # <editor-fold desc="View page"> 4162 def display_view_page(self) -> None: 4163 """Displays the edit project page.""" 4164 if self.is_distance_plot_open: 4165 self.distance_plot_dialog.close() 4166 self.is_distance_plot_open = False 4167 self._view.ui.list_view_project_proteins.clear() 4168 self._view.ui.txtedit_view_sequence.clear() 4169 # pre-process 4170 self._view.status_bar.showMessage(self._workspace_label.text()) 4171 # list all proteins from pdb directory 4172 gui_utils.fill_list_view_with_protein_names(self._current_project, self._view.ui.list_view_project_proteins) 4173 4174 tools.switch_page( 4175 self._view.ui.stackedWidget, 4176 self._view.ui.lbl_page_title, 4177 11, 4178 "View proteins of current project", 4179 ) 4180 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_view_page) 4181 gui_elements_to_hide = [ 4182 self._view.ui.btn_view_project_show, 4183 self._view.ui.btn_view_project_show_structure, 4184 self._view.ui.txtedit_view_sequence, 4185 self._view.ui.label_9, 4186 self._view.ui.label_11, 4187 ] 4188 gui_utils.hide_gui_elements(gui_elements_to_hide) 4189 4190 def view_show_options(self) -> None: 4191 """Controls which gui elements get shown.""" 4192 gui_elements_to_show = [ 4193 # self._view.ui.btn_view_project_show, 4194 self._view.ui.btn_view_project_show_structure, 4195 self._view.ui.txtedit_view_sequence, 4196 # self._view.ui.label_9, 4197 self._view.ui.label_11, 4198 ] 4199 gui_utils.show_gui_elements(gui_elements_to_show) 4200 self.view_sequence() 4201 4202 def view_sequence(self) -> None: 4203 """Displays the sequence of the selected protein in a text box.""" 4204 tmp_protein_basename = self._view.ui.list_view_project_proteins.currentItem().text() 4205 tmp_protein_sequences = self._current_project.search_protein(tmp_protein_basename).get_protein_sequences() 4206 self._view.ui.txtedit_view_sequence.clear() 4207 for tmp_sequence in tmp_protein_sequences: 4208 self._view.ui.txtedit_view_sequence.append("".join(tmp_sequence.sequence)) 4209 # fixme: experimental sequence viewer gui 4210 # dialog = dialog_sequence_viewer.SequenceViewer(tmp_protein_sequences, tmp_protein_filename) 4211 # dialog.exec_() 4212 4213 # </editor-fold> 4214 4215 # <editor-fold desc="Use page"> 4216 def validate_use_project_name(self) -> None: 4217 """Validates the input of the project name in real-time.""" 4218 input_validator.InputValidator.validate_project_name( 4219 self._view.ui.list_use_existing_projects, 4220 self._view.ui.txt_use_project_name, 4221 self._view.ui.lbl_use_status_project_name, 4222 self._view.ui.btn_use_next, 4223 ) 4224 4225 def validate_use_search(self) -> None: 4226 """Validates the input of the protein name in real-time.""" 4227 message = "Protein structure does not exists." 4228 input_validator.InputValidator.validate_search_input( 4229 self._view.ui.list_use_available_protein_structures, 4230 self._view.ui.txt_use_search, 4231 self._view.ui.lbl_use_status_search, 4232 status_message=message, 4233 ) 4234 4235 def add_protein_structure_to_new_project(self) -> None: 4236 """Adds the selected protein to the list which is used to create the new project.""" 4237 prot_to_add = self._view.ui.list_use_available_protein_structures.currentItem().text() 4238 self._view.ui.list_use_selected_protein_structures.addItem(prot_to_add) 4239 self._view.ui.list_use_available_protein_structures.takeItem( 4240 self._view.ui.list_use_available_protein_structures.currentRow(), 4241 ) 4242 self._view.ui.btn_use_add_available_protein_structures.setEnabled(False) 4243 if self._view.ui.list_use_available_protein_structures.count() > 0: 4244 try: 4245 self._view.ui.list_use_available_protein_structures.currentItem().setSelected(False) 4246 except AttributeError: 4247 constants.PYSSA_LOGGER.debug("No selection in use available proteins list on Use page.") 4248 4249 def remove_protein_structure_to_new_project(self) -> None: 4250 """Removes the selected protein from the list which is used to create the new project.""" 4251 prot_to_remove = self._view.ui.list_use_selected_protein_structures.currentItem() 4252 self._view.ui.list_use_selected_protein_structures.takeItem( 4253 self._view.ui.list_use_selected_protein_structures.currentRow(), 4254 ) 4255 self._view.ui.list_use_available_protein_structures.addItem(prot_to_remove) 4256 self._view.ui.btn_use_remove_selected_protein_structures.setEnabled(False) 4257 if self._view.ui.list_use_selected_protein_structures.count() > 0: 4258 try: 4259 self._view.ui.list_use_selected_protein_structures.currentItem().setSelected(False) 4260 except AttributeError: 4261 constants.PYSSA_LOGGER.debug("No selection in use selected proteins list on Use page.") 4262 4263 def show_protein_selection_for_use(self) -> None: 4264 """Shows the two lists for the protein selection.""" 4265 gui_elements_to_show = [ 4266 self._view.ui.lbl_use_search, 4267 self._view.ui.lbl_use_status_search, 4268 self._view.ui.txt_use_search, 4269 self._view.ui.btn_use_add_available_protein_structures, 4270 self._view.ui.lbl_use_available_protein_structures, 4271 self._view.ui.list_use_available_protein_structures, 4272 self._view.ui.btn_use_remove_selected_protein_structures, 4273 self._view.ui.lbl_use_selected_protein_structures, 4274 self._view.ui.list_use_selected_protein_structures, 4275 self._view.ui.btn_use_back, 4276 self._view.ui.btn_use_create_new_project, 4277 self._view.ui.lbl_use_new_project, 4278 ] 4279 gui_utils.show_gui_elements(gui_elements_to_show) 4280 self._view.ui.txt_use_project_name.setEnabled(False) 4281 gui_elements_to_hide = [ 4282 self._view.ui.btn_use_next, 4283 self._view.ui.list_use_existing_projects, 4284 ] 4285 gui_utils.hide_gui_elements(gui_elements_to_hide) 4286 gui_utils.disable_text_box(self._view.ui.txt_use_project_name, self._view.ui.lbl_use_project_name) 4287 self._view.ui.btn_use_add_available_protein_structures.setEnabled(False) 4288 self._view.ui.btn_use_remove_selected_protein_structures.setEnabled(False) 4289 4290 def hide_protein_selection_for_use(self) -> None: 4291 """Hides the two lists for the protein selection.""" 4292 gui_elements_to_show = [ 4293 self._view.ui.btn_use_next, 4294 self._view.ui.list_use_existing_projects, 4295 ] 4296 gui_utils.show_gui_elements(gui_elements_to_show) 4297 self._view.ui.txt_use_project_name.setEnabled(True) 4298 4299 gui_elements_to_hide = [ 4300 self._view.ui.lbl_use_search, 4301 self._view.ui.lbl_use_status_search, 4302 self._view.ui.txt_use_search, 4303 self._view.ui.btn_use_add_available_protein_structures, 4304 self._view.ui.lbl_use_available_protein_structures, 4305 self._view.ui.list_use_available_protein_structures, 4306 self._view.ui.btn_use_remove_selected_protein_structures, 4307 self._view.ui.lbl_use_selected_protein_structures, 4308 self._view.ui.list_use_selected_protein_structures, 4309 self._view.ui.btn_use_back, 4310 self._view.ui.btn_use_create_new_project, 4311 self._view.ui.lbl_use_new_project, 4312 ] 4313 gui_utils.hide_gui_elements(gui_elements_to_hide) 4314 gui_utils.enable_text_box(self._view.ui.txt_use_project_name, self._view.ui.lbl_use_project_name) 4315 4316 def use_enable_add(self) -> None: 4317 """Enables the add button.""" 4318 self._view.ui.btn_use_add_available_protein_structures.setEnabled(True) 4319 4320 def use_enable_remove(self) -> None: 4321 """Enables the remove button.""" 4322 self._view.ui.btn_use_remove_selected_protein_structures.setEnabled(True) 4323 4324 # </editor-fold> 4325 4326 # <editor-fold desc="ESM fold"> 4327 def _init_esm_pred_mono_page(self) -> None: 4328 """Clears all text boxes and sets up the default values for the page.""" 4329 # clears everything 4330 self._view.ui.txt_esm_prot_name.clear() 4331 self._view.ui.txt_esm_prot_seq.clear() 4332 for i in range(self._view.ui.table_esm_prot_to_predict.rowCount()): 4333 self._view.ui.table_esm_prot_to_predict.removeRow(i) 4334 # sets up defaults: Prediction 4335 self._view.ui.btn_esm_next.setEnabled(False) 4336 self._view.ui.btn_esm_next_2.setEnabled(False) 4337 self._view.ui.lbl_esm_prot_name_status.setText("") 4338 self._view.ui.lbl_esm_prot_seq_status.setText("") 4339 4340 def display_esm_pred_mono(self) -> None: 4341 """Displays the esm_fold monomer page.""" 4342 self._init_esm_pred_mono_page() 4343 gui_elements_to_show = [ 4344 self._view.ui.lbl_esm_prot_to_predict, 4345 self._view.ui.table_esm_prot_to_predict, 4346 self._view.ui.btn_esm_seq_to_predict, 4347 ] 4348 gui_elements_to_hide = [ 4349 self._view.ui.btn_esm_seq_to_predict_remove, 4350 self._view.ui.lbl_esm_prot_name, 4351 self._view.ui.txt_esm_prot_name, 4352 self._view.ui.lbl_esm_prot_name_status, 4353 self._view.ui.btn_esm_back, 4354 self._view.ui.btn_esm_next, 4355 self._view.ui.lbl_esm_prot_seq, 4356 self._view.ui.txt_esm_prot_seq, 4357 self._view.ui.lbl_esm_prot_seq_status, 4358 self._view.ui.btn_esm_back_2, 4359 self._view.ui.btn_esm_next_2, 4360 self._view.ui.btn_esm_predict, 4361 ] 4362 gui_utils.show_gui_elements(gui_elements_to_show) 4363 gui_utils.hide_gui_elements(gui_elements_to_hide) 4364 styles.color_button_not_ready(self._view.ui.btn_esm_next) 4365 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 1, "ESMFold Monomer Prediction") 4366 self.last_sidebar_button = styles.color_sidebar_buttons( 4367 self.last_sidebar_button, 4368 self._view.ui.btn_pred_cloud_monomer_page, 4369 ) 4370 4371 def cloud_esm_validate_protein_name(self) -> None: 4372 """Validates the input of the protein name in real-time.""" 4373 if safeguard.Safeguard.check_if_value_is_in_table_v_header( 4374 self._view.ui.txt_esm_prot_name.text(), 4375 self._view.ui.table_esm_prot_to_predict, 4376 ): 4377 self._view.ui.lbl_esm_prot_name_status.setText("Protein name already used.") 4378 self._view.ui.btn_esm_next.setEnabled(False) 4379 styles.color_button_not_ready(self._view.ui.btn_esm_next) 4380 else: 4381 self._view.ui.btn_esm_next.setEnabled(True) 4382 tools.validate_protein_name( 4383 self._view.ui.txt_esm_prot_name, 4384 self._view.ui.lbl_esm_prot_name_status, 4385 self._view.ui.btn_esm_next, 4386 ) 4387 4388 def cloud_esm_validate_protein_sequence(self) -> None: 4389 """Validates the input of the protein sequence in real-time.""" 4390 tools.validate_protein_sequence( 4391 self._view.ui.txt_esm_prot_seq, 4392 self._view.ui.lbl_esm_prot_seq_status, 4393 self._view.ui.btn_esm_next_2, 4394 ) 4395 4396 def setup_defaults_esm_monomer_prediction(self) -> None: 4397 """Sets up the default values for the page.""" 4398 # clears everything 4399 self._view.ui.txt_esm_prot_name.clear() 4400 self._view.ui.txt_esm_prot_seq.clear() 4401 # sets up defaults: Prediction 4402 self._view.ui.btn_esm_next.setEnabled(False) 4403 self._view.ui.btn_esm_next_2.setEnabled(False) 4404 self._view.ui.lbl_esm_prot_name_status.setText("") 4405 self._view.ui.lbl_esm_prot_seq_status.setText("") 4406 4407 def cloud_esm_add_seq_to_predict(self) -> None: 4408 """Shows the gui elements to add a sequence to the protein to predict.""" 4409 gui_elements_to_show = [ 4410 self._view.ui.lbl_esm_prot_to_predict, 4411 self._view.ui.table_esm_prot_to_predict, 4412 self._view.ui.lbl_esm_prot_name, 4413 self._view.ui.txt_esm_prot_name, 4414 self._view.ui.lbl_esm_prot_name_status, 4415 self._view.ui.btn_esm_back, 4416 self._view.ui.btn_esm_next, 4417 ] 4418 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4419 gui_elements_to_hide = [ 4420 self._view.ui.btn_esm_seq_to_predict_remove, 4421 self._view.ui.btn_esm_seq_to_predict, 4422 self._view.ui.lbl_esm_prot_seq, 4423 self._view.ui.txt_esm_prot_seq, 4424 self._view.ui.lbl_esm_prot_seq_status, 4425 self._view.ui.btn_esm_back_2, 4426 self._view.ui.btn_esm_next_2, 4427 self._view.ui.btn_esm_predict, 4428 ] 4429 gui_utils.disable_text_box(self._view.ui.txt_esm_prot_seq, self._view.ui.lbl_esm_prot_seq) 4430 gui_utils.show_gui_elements(gui_elements_to_show) 4431 gui_utils.hide_gui_elements(gui_elements_to_hide) 4432 self._view.ui.btn_esm_next.setEnabled(False) 4433 self._view.ui.txt_esm_prot_name.clear() 4434 styles.color_button_not_ready(self._view.ui.btn_esm_next) 4435 if self._view.ui.table_esm_prot_to_predict.rowCount() > 0: 4436 try: 4437 self._view.ui.table_esm_prot_to_predict.currentItem().setSelected(False) 4438 except AttributeError: 4439 constants.PYSSA_LOGGER.debug("No selection on Local Monomer Prediction in overview table.") 4440 4441 def cloud_esm_back(self) -> None: 4442 """Hides the gui elements for the protein name.""" 4443 gui_elements_to_show = [ 4444 self._view.ui.lbl_esm_prot_to_predict, 4445 self._view.ui.table_esm_prot_to_predict, 4446 self._view.ui.btn_esm_seq_to_predict_remove, 4447 self._view.ui.btn_esm_seq_to_predict, 4448 ] 4449 gui_elements_to_hide = [ 4450 self._view.ui.lbl_esm_prot_name, 4451 self._view.ui.txt_esm_prot_name, 4452 self._view.ui.lbl_esm_prot_name_status, 4453 self._view.ui.btn_esm_back, 4454 self._view.ui.btn_esm_next, 4455 self._view.ui.lbl_esm_prot_seq, 4456 self._view.ui.txt_esm_prot_seq, 4457 self._view.ui.lbl_esm_prot_seq_status, 4458 self._view.ui.btn_esm_back_2, 4459 self._view.ui.btn_esm_next_2, 4460 self._view.ui.btn_esm_predict, 4461 ] 4462 gui_utils.show_gui_elements(gui_elements_to_show) 4463 gui_utils.hide_gui_elements(gui_elements_to_hide) 4464 self.cloud_esm_check_if_table_is_empty() 4465 self._view.ui.btn_esm_seq_to_predict_remove.setEnabled(False) 4466 4467 def cloud_esm_next(self) -> None: 4468 """Shows the gui elements for the protein name.""" 4469 gui_elements_to_show = [ 4470 self._view.ui.lbl_esm_prot_to_predict, 4471 self._view.ui.table_esm_prot_to_predict, 4472 self._view.ui.lbl_esm_prot_name, 4473 self._view.ui.txt_esm_prot_name, 4474 self._view.ui.lbl_esm_prot_seq, 4475 self._view.ui.txt_esm_prot_seq, 4476 self._view.ui.lbl_esm_prot_seq_status, 4477 self._view.ui.btn_esm_back_2, 4478 self._view.ui.btn_esm_next_2, 4479 ] 4480 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_seq, self._view.ui.lbl_esm_prot_seq) 4481 gui_elements_to_hide = [ 4482 self._view.ui.btn_esm_seq_to_predict_remove, 4483 self._view.ui.btn_esm_seq_to_predict, 4484 self._view.ui.lbl_esm_prot_name_status, 4485 self._view.ui.btn_esm_back, 4486 self._view.ui.btn_esm_next, 4487 self._view.ui.btn_esm_predict, 4488 ] 4489 gui_utils.disable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4490 gui_utils.show_gui_elements(gui_elements_to_show) 4491 gui_utils.hide_gui_elements(gui_elements_to_hide) 4492 self._view.ui.txt_esm_prot_seq.clear() 4493 4494 def cloud_esm_back_2(self) -> None: 4495 """Hides the gui elements for the protein sequence.""" 4496 gui_elements_to_show = [ 4497 self._view.ui.lbl_esm_prot_to_predict, 4498 self._view.ui.table_esm_prot_to_predict, 4499 self._view.ui.lbl_esm_prot_name, 4500 self._view.ui.txt_esm_prot_name, 4501 self._view.ui.lbl_esm_prot_name_status, 4502 self._view.ui.btn_esm_back, 4503 self._view.ui.btn_esm_next, 4504 ] 4505 gui_elements_to_hide = [ 4506 self._view.ui.btn_esm_seq_to_predict_remove, 4507 self._view.ui.btn_esm_seq_to_predict, 4508 self._view.ui.lbl_esm_prot_seq, 4509 self._view.ui.txt_esm_prot_seq, 4510 self._view.ui.lbl_esm_prot_seq_status, 4511 self._view.ui.btn_esm_back_2, 4512 self._view.ui.btn_esm_next_2, 4513 self._view.ui.btn_esm_predict, 4514 ] 4515 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4516 gui_utils.disable_text_box(self._view.ui.txt_esm_prot_seq, self._view.ui.lbl_esm_prot_seq) 4517 gui_utils.show_gui_elements(gui_elements_to_show) 4518 gui_utils.hide_gui_elements(gui_elements_to_hide) 4519 4520 def cloud_esm_add_protein(self) -> None: 4521 """Adds protein to the list of proteins to predict.""" 4522 self._view.ui.table_esm_prot_to_predict.setRowCount(self._view.ui.table_esm_prot_to_predict.rowCount() + 1) 4523 self._view.ui.table_esm_prot_to_predict.insertRow(self._view.ui.table_esm_prot_to_predict.rowCount() + 1) 4524 self._view.ui.table_esm_prot_to_predict.setItem( 4525 self._view.ui.table_esm_prot_to_predict.rowCount() - 1, 4526 0, 4527 QtWidgets.QTableWidgetItem("A"), 4528 ) 4529 self._view.ui.table_esm_prot_to_predict.setItem( 4530 self._view.ui.table_esm_prot_to_predict.rowCount() - 1, 4531 1, 4532 QtWidgets.QTableWidgetItem(self._view.ui.txt_esm_prot_seq.toPlainText()), 4533 ) 4534 self._view.ui.table_esm_prot_to_predict.setVerticalHeaderItem( 4535 self._view.ui.table_esm_prot_to_predict.rowCount() - 1, 4536 QtWidgets.QTableWidgetItem(self._view.ui.txt_esm_prot_name.text()), 4537 ) 4538 self._view.ui.table_esm_prot_to_predict.resizeColumnsToContents() 4539 self.cloud_esm_check_if_table_is_empty() 4540 gui_elements_to_show = [ 4541 self._view.ui.lbl_esm_prot_to_predict, 4542 self._view.ui.table_esm_prot_to_predict, 4543 self._view.ui.btn_esm_seq_to_predict_remove, 4544 self._view.ui.btn_esm_seq_to_predict, 4545 self._view.ui.btn_esm_predict, 4546 ] 4547 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4548 gui_elements_to_hide = [ 4549 self._view.ui.lbl_esm_prot_name, 4550 self._view.ui.txt_esm_prot_name, 4551 self._view.ui.lbl_esm_prot_name_status, 4552 self._view.ui.btn_esm_back, 4553 self._view.ui.btn_esm_next, 4554 self._view.ui.lbl_esm_prot_seq, 4555 self._view.ui.txt_esm_prot_seq, 4556 self._view.ui.lbl_esm_prot_seq_status, 4557 self._view.ui.btn_esm_back_2, 4558 self._view.ui.btn_esm_next_2, 4559 ] 4560 gui_utils.show_gui_elements(gui_elements_to_show) 4561 gui_utils.hide_gui_elements(gui_elements_to_hide) 4562 self._view.ui.btn_esm_predict.setEnabled(True) 4563 self._view.ui.btn_esm_seq_to_predict_remove.setEnabled(False) 4564 self.setup_defaults_esm_monomer_prediction() 4565 4566 def cloud_esm_remove(self) -> None: 4567 """Removes a protein from the list of proteins to predict.""" 4568 self._view.ui.table_esm_prot_to_predict.removeRow(self._view.ui.table_esm_prot_to_predict.currentRow()) 4569 gui_elements_to_show = [ 4570 self._view.ui.lbl_esm_prot_to_predict, 4571 self._view.ui.table_esm_prot_to_predict, 4572 self._view.ui.btn_esm_seq_to_predict_remove, 4573 self._view.ui.btn_esm_seq_to_predict, 4574 self._view.ui.btn_esm_predict, 4575 ] 4576 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4577 gui_elements_to_hide = [ 4578 self._view.ui.lbl_esm_prot_name, 4579 self._view.ui.txt_esm_prot_name, 4580 self._view.ui.lbl_esm_prot_name_status, 4581 self._view.ui.btn_esm_back, 4582 self._view.ui.btn_esm_next, 4583 self._view.ui.lbl_esm_prot_seq, 4584 self._view.ui.txt_esm_prot_seq, 4585 self._view.ui.lbl_esm_prot_seq_status, 4586 self._view.ui.btn_esm_back_2, 4587 self._view.ui.btn_esm_next_2, 4588 ] 4589 gui_utils.show_gui_elements(gui_elements_to_show) 4590 gui_utils.hide_gui_elements(gui_elements_to_hide) 4591 self._view.ui.btn_esm_seq_to_predict_remove.setEnabled(False) 4592 self.cloud_esm_check_if_table_is_empty() 4593 4594 def cloud_esm_item_changed(self) -> None: 4595 """Enables the remove button.""" 4596 self._view.ui.btn_esm_seq_to_predict_remove.setEnabled(True) 4597 4598 def cloud_esm_check_if_table_is_empty(self) -> None: 4599 """Checks if the table proteins to predict is empty.""" 4600 if self._view.ui.table_esm_prot_to_predict.rowCount() == 0: 4601 styles.color_button_not_ready(self._view.ui.btn_esm_predict) 4602 self._view.ui.btn_esm_predict.setEnabled(False) 4603 gui_elements_to_show = [ 4604 self._view.ui.lbl_esm_prot_to_predict, 4605 self._view.ui.table_esm_prot_to_predict, 4606 self._view.ui.btn_esm_seq_to_predict, 4607 ] 4608 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4609 gui_elements_to_hide = [ 4610 self._view.ui.btn_esm_seq_to_predict_remove, 4611 self._view.ui.lbl_esm_prot_name, 4612 self._view.ui.txt_esm_prot_name, 4613 self._view.ui.lbl_esm_prot_name_status, 4614 self._view.ui.btn_esm_back, 4615 self._view.ui.btn_esm_next, 4616 self._view.ui.lbl_esm_prot_seq, 4617 self._view.ui.txt_esm_prot_seq, 4618 self._view.ui.lbl_esm_prot_seq_status, 4619 self._view.ui.btn_esm_back_2, 4620 self._view.ui.btn_esm_next_2, 4621 self._view.ui.btn_esm_predict, 4622 ] 4623 gui_utils.show_gui_elements(gui_elements_to_show) 4624 gui_utils.hide_gui_elements(gui_elements_to_hide) 4625 else: 4626 self._view.ui.btn_esm_predict.setEnabled(True) 4627 4628 # </editor-fold> 4629 4630 # <editor-fold desc="Monomer local prediction"> 4631 def _init_local_pred_mono_page(self) -> None: 4632 """Clears all text boxes and sets default values for the gui elements.""" 4633 # clears everything 4634 self._view.ui.txt_pred_mono_prot_name.clear() 4635 self._view.ui.txt_pred_mono_seq_name.clear() 4636 for i in range(self._view.ui.table_pred_mono_prot_to_predict.rowCount()): 4637 self._view.ui.table_pred_mono_prot_to_predict.removeRow(i) 4638 # sets up defaults: Prediction 4639 self._view.ui.btn_pred_mono_next.setEnabled(False) 4640 self._view.ui.btn_pred_mono_add_protein.setEnabled(False) 4641 self._view.ui.lbl_pred_mono_prot_name_status.setText("") 4642 self._view.ui.lbl_pred_mono_seq_name_status.setText("") 4643 4644 def display_local_pred_mono(self) -> None: 4645 """Displays the local prediction monomer page.""" 4646 # checks internet connection 4647 if not tools.check_internet_connectivity(): 4648 gui_utils.no_internet_dialog() 4649 return 4650 self._init_local_pred_mono_page() 4651 gui_elements_to_show = [ 4652 self._view.ui.lbl_pred_mono_prot_to_predict, 4653 self._view.ui.table_pred_mono_prot_to_predict, 4654 self._view.ui.btn_pred_mono_seq_to_predict, 4655 ] 4656 gui_elements_to_hide = [ 4657 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4658 self._view.ui.lbl_pred_mono_prot_name, 4659 self._view.ui.txt_pred_mono_prot_name, 4660 self._view.ui.lbl_pred_mono_prot_name_status, 4661 self._view.ui.btn_pred_mono_back, 4662 self._view.ui.btn_pred_mono_next, 4663 self._view.ui.lbl_pred_mono_seq_name, 4664 self._view.ui.txt_pred_mono_seq_name, 4665 self._view.ui.lbl_pred_mono_seq_name_status, 4666 self._view.ui.btn_pred_mono_back_2, 4667 self._view.ui.btn_pred_mono_add_protein, 4668 self._view.ui.lbl_pred_mono_advanced_config, 4669 self._view.ui.btn_pred_mono_advanced_config, 4670 self._view.ui.btn_pred_mono_predict, 4671 ] 4672 gui_utils.show_gui_elements(gui_elements_to_show) 4673 gui_utils.hide_gui_elements(gui_elements_to_hide) 4674 styles.color_button_not_ready(self._view.ui.btn_pred_mono_next) 4675 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 19, "Local Monomer Prediction") 4676 self.last_sidebar_button = styles.color_sidebar_buttons( 4677 self.last_sidebar_button, 4678 self._view.ui.btn_pred_local_monomer_page, 4679 ) 4680 4681 def local_pred_mono_validate_protein_name(self) -> None: 4682 """Validates the input of the protein name in real-time.""" 4683 if safeguard.Safeguard.check_if_value_is_in_table_v_header( 4684 self._view.ui.txt_pred_mono_prot_name.text(), 4685 self._view.ui.table_pred_mono_prot_to_predict, 4686 ): 4687 self._view.ui.lbl_pred_mono_prot_name_status.setText("Protein name already used.") 4688 self._view.ui.btn_pred_mono_next.setEnabled(False) 4689 styles.color_button_not_ready(self._view.ui.btn_pred_mono_next) 4690 else: 4691 self._view.ui.btn_pred_mono_next.setEnabled(True) 4692 tools.validate_protein_name( 4693 self._view.ui.txt_pred_mono_prot_name, 4694 self._view.ui.lbl_pred_mono_prot_name_status, 4695 self._view.ui.btn_pred_mono_next, 4696 ) 4697 4698 def local_pred_mono_validate_protein_sequence(self) -> None: 4699 """Validates the input of the protein sequence in real-time.""" 4700 tools.validate_protein_sequence( 4701 self._view.ui.txt_pred_mono_seq_name, 4702 self._view.ui.lbl_pred_mono_seq_name_status, 4703 self._view.ui.btn_pred_mono_add_protein, 4704 ) 4705 4706 def show_prediction_configuration(self) -> None: 4707 """Opens the prediction configuration dialog window.""" 4708 config = dialog_advanced_prediction_configurations.DialogAdvancedPredictionConfigurations( 4709 self.prediction_configuration, 4710 ) 4711 config.exec_() 4712 self.prediction_configuration.amber_force_field = config.prediction_config.amber_force_field 4713 self.prediction_configuration.templates = config.prediction_config.templates 4714 4715 def setup_defaults_monomer_prediction(self) -> None: 4716 """Sets up the defaults for the page.""" 4717 # clears everything 4718 self._view.ui.txt_pred_mono_prot_name.clear() 4719 self._view.ui.txt_pred_mono_seq_name.clear() 4720 # sets up defaults: Prediction 4721 self._view.ui.btn_pred_mono_next.setEnabled(False) 4722 self._view.ui.btn_pred_mono_add_protein.setEnabled(False) 4723 self._view.ui.lbl_pred_mono_prot_name_status.setText("") 4724 self._view.ui.lbl_pred_mono_seq_name_status.setText("") 4725 4726 def local_pred_mono_add_seq_to_predict(self) -> None: 4727 """Shows the gui elements for the protein name.""" 4728 gui_elements_to_show = [ 4729 self._view.ui.lbl_pred_mono_prot_to_predict, 4730 self._view.ui.table_pred_mono_prot_to_predict, 4731 self._view.ui.lbl_pred_mono_prot_name, 4732 self._view.ui.txt_pred_mono_prot_name, 4733 self._view.ui.lbl_pred_mono_prot_name_status, 4734 self._view.ui.btn_pred_mono_back, 4735 self._view.ui.btn_pred_mono_next, 4736 ] 4737 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4738 gui_elements_to_hide = [ 4739 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4740 self._view.ui.btn_pred_mono_seq_to_predict, 4741 self._view.ui.lbl_pred_mono_seq_name, 4742 self._view.ui.txt_pred_mono_seq_name, 4743 self._view.ui.lbl_pred_mono_seq_name_status, 4744 self._view.ui.btn_pred_mono_back_2, 4745 self._view.ui.btn_pred_mono_add_protein, 4746 self._view.ui.lbl_pred_mono_advanced_config, 4747 self._view.ui.btn_pred_mono_advanced_config, 4748 self._view.ui.btn_pred_mono_predict, 4749 ] 4750 gui_utils.disable_text_box(self._view.ui.txt_pred_mono_seq_name, self._view.ui.lbl_pred_mono_seq_name) 4751 gui_utils.show_gui_elements(gui_elements_to_show) 4752 gui_utils.hide_gui_elements(gui_elements_to_hide) 4753 self._view.ui.btn_pred_mono_next.setEnabled(False) 4754 self._view.ui.txt_pred_mono_prot_name.clear() 4755 styles.color_button_not_ready(self._view.ui.btn_pred_mono_next) 4756 if self._view.ui.table_pred_mono_prot_to_predict.rowCount() > 0: 4757 try: 4758 self._view.ui.table_pred_mono_prot_to_predict.currentItem().setSelected(False) 4759 except AttributeError: 4760 constants.PYSSA_LOGGER.debug("No selection on Local Monomer Prediction in overview table.") 4761 4762 def local_pred_mono_back(self) -> None: 4763 """Hides the gui elements for the protein name.""" 4764 gui_elements_to_show = [ 4765 self._view.ui.lbl_pred_mono_prot_to_predict, 4766 self._view.ui.table_pred_mono_prot_to_predict, 4767 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4768 self._view.ui.btn_pred_mono_seq_to_predict, 4769 ] 4770 gui_elements_to_hide = [ 4771 self._view.ui.lbl_pred_mono_prot_name, 4772 self._view.ui.txt_pred_mono_prot_name, 4773 self._view.ui.lbl_pred_mono_prot_name_status, 4774 self._view.ui.btn_pred_mono_back, 4775 self._view.ui.btn_pred_mono_next, 4776 self._view.ui.lbl_pred_mono_seq_name, 4777 self._view.ui.txt_pred_mono_seq_name, 4778 self._view.ui.lbl_pred_mono_seq_name_status, 4779 self._view.ui.btn_pred_mono_back_2, 4780 self._view.ui.btn_pred_mono_add_protein, 4781 self._view.ui.lbl_pred_mono_advanced_config, 4782 self._view.ui.btn_pred_mono_advanced_config, 4783 self._view.ui.btn_pred_mono_predict, 4784 ] 4785 gui_utils.show_gui_elements(gui_elements_to_show) 4786 gui_utils.hide_gui_elements(gui_elements_to_hide) 4787 self.local_pred_mono_check_if_table_is_empty() 4788 self._view.ui.btn_pred_mono_seq_to_predict_remove.setEnabled(False) 4789 4790 def local_pred_mono_next(self) -> None: 4791 """Shows the gui elements for the protein sequence.""" 4792 gui_elements_to_show = [ 4793 self._view.ui.lbl_pred_mono_prot_to_predict, 4794 self._view.ui.table_pred_mono_prot_to_predict, 4795 self._view.ui.lbl_pred_mono_prot_name, 4796 self._view.ui.txt_pred_mono_prot_name, 4797 self._view.ui.lbl_pred_mono_seq_name, 4798 self._view.ui.txt_pred_mono_seq_name, 4799 self._view.ui.lbl_pred_mono_seq_name_status, 4800 self._view.ui.btn_pred_mono_back_2, 4801 self._view.ui.btn_pred_mono_add_protein, 4802 ] 4803 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_seq_name, self._view.ui.lbl_pred_mono_seq_name) 4804 gui_elements_to_hide = [ 4805 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4806 self._view.ui.btn_pred_mono_seq_to_predict, 4807 self._view.ui.lbl_pred_mono_prot_name_status, 4808 self._view.ui.btn_pred_mono_back, 4809 self._view.ui.btn_pred_mono_next, 4810 self._view.ui.lbl_pred_mono_advanced_config, 4811 self._view.ui.btn_pred_mono_advanced_config, 4812 self._view.ui.btn_pred_mono_predict, 4813 ] 4814 gui_utils.disable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4815 gui_utils.show_gui_elements(gui_elements_to_show) 4816 gui_utils.hide_gui_elements(gui_elements_to_hide) 4817 self._view.ui.txt_pred_mono_seq_name.clear() 4818 4819 def local_pred_mono_back_2(self) -> None: 4820 """Hides the gui elements for the protein sequence.""" 4821 gui_elements_to_show = [ 4822 self._view.ui.lbl_pred_mono_prot_to_predict, 4823 self._view.ui.table_pred_mono_prot_to_predict, 4824 self._view.ui.lbl_pred_mono_prot_name, 4825 self._view.ui.txt_pred_mono_prot_name, 4826 self._view.ui.lbl_pred_mono_prot_name_status, 4827 self._view.ui.btn_pred_mono_back, 4828 self._view.ui.btn_pred_mono_next, 4829 ] 4830 gui_elements_to_hide = [ 4831 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4832 self._view.ui.btn_pred_mono_seq_to_predict, 4833 self._view.ui.lbl_pred_mono_seq_name, 4834 self._view.ui.txt_pred_mono_seq_name, 4835 self._view.ui.lbl_pred_mono_seq_name_status, 4836 self._view.ui.btn_pred_mono_back_2, 4837 self._view.ui.btn_pred_mono_add_protein, 4838 self._view.ui.lbl_pred_mono_advanced_config, 4839 self._view.ui.btn_pred_mono_advanced_config, 4840 self._view.ui.btn_pred_mono_predict, 4841 ] 4842 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4843 gui_utils.disable_text_box(self._view.ui.txt_pred_mono_seq_name, self._view.ui.lbl_pred_mono_seq_name) 4844 gui_utils.show_gui_elements(gui_elements_to_show) 4845 gui_utils.hide_gui_elements(gui_elements_to_hide) 4846 4847 def local_pred_mono_add_protein(self) -> None: 4848 """Adds protein to the list of proteins to predict.""" 4849 self._view.ui.table_pred_mono_prot_to_predict.setRowCount( 4850 self._view.ui.table_pred_mono_prot_to_predict.rowCount() + 1, 4851 ) 4852 self._view.ui.table_pred_mono_prot_to_predict.insertRow( 4853 self._view.ui.table_pred_mono_prot_to_predict.rowCount() + 1, 4854 ) 4855 self._view.ui.table_pred_mono_prot_to_predict.setItem( 4856 self._view.ui.table_pred_mono_prot_to_predict.rowCount() - 1, 4857 0, 4858 QtWidgets.QTableWidgetItem("A"), 4859 ) 4860 self._view.ui.table_pred_mono_prot_to_predict.setItem( 4861 self._view.ui.table_pred_mono_prot_to_predict.rowCount() - 1, 4862 1, 4863 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_mono_seq_name.toPlainText()), 4864 ) 4865 self._view.ui.table_pred_mono_prot_to_predict.setVerticalHeaderItem( 4866 self._view.ui.table_pred_mono_prot_to_predict.rowCount() - 1, 4867 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_mono_prot_name.text()), 4868 ) 4869 self._view.ui.table_pred_mono_prot_to_predict.resizeColumnsToContents() 4870 self.local_pred_mono_check_if_table_is_empty() 4871 gui_elements_to_show = [ 4872 self._view.ui.lbl_pred_mono_prot_to_predict, 4873 self._view.ui.table_pred_mono_prot_to_predict, 4874 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4875 self._view.ui.btn_pred_mono_seq_to_predict, 4876 self._view.ui.lbl_pred_mono_advanced_config, 4877 self._view.ui.btn_pred_mono_advanced_config, 4878 self._view.ui.btn_pred_mono_predict, 4879 ] 4880 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4881 gui_elements_to_hide = [ 4882 self._view.ui.lbl_pred_mono_prot_name, 4883 self._view.ui.txt_pred_mono_prot_name, 4884 self._view.ui.lbl_pred_mono_prot_name_status, 4885 self._view.ui.btn_pred_mono_back, 4886 self._view.ui.btn_pred_mono_next, 4887 self._view.ui.lbl_pred_mono_seq_name, 4888 self._view.ui.txt_pred_mono_seq_name, 4889 self._view.ui.lbl_pred_mono_seq_name_status, 4890 self._view.ui.btn_pred_mono_back_2, 4891 self._view.ui.btn_pred_mono_add_protein, 4892 ] 4893 gui_utils.show_gui_elements(gui_elements_to_show) 4894 gui_utils.hide_gui_elements(gui_elements_to_hide) 4895 self._view.ui.btn_pred_mono_predict.setEnabled(True) 4896 self._view.ui.btn_pred_mono_seq_to_predict_remove.setEnabled(False) 4897 self.setup_defaults_monomer_prediction() 4898 4899 def local_pred_mono_remove(self) -> None: 4900 """Removes the selected protein from the list of proteins to predict.""" 4901 self._view.ui.table_pred_mono_prot_to_predict.removeRow( 4902 self._view.ui.table_pred_mono_prot_to_predict.currentRow(), 4903 ) 4904 gui_elements_to_show = [ 4905 self._view.ui.lbl_pred_mono_prot_to_predict, 4906 self._view.ui.table_pred_mono_prot_to_predict, 4907 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4908 self._view.ui.btn_pred_mono_seq_to_predict, 4909 self._view.ui.lbl_pred_mono_advanced_config, 4910 self._view.ui.btn_pred_mono_advanced_config, 4911 self._view.ui.btn_pred_mono_predict, 4912 ] 4913 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4914 gui_elements_to_hide = [ 4915 self._view.ui.lbl_pred_mono_prot_name, 4916 self._view.ui.txt_pred_mono_prot_name, 4917 self._view.ui.lbl_pred_mono_prot_name_status, 4918 self._view.ui.btn_pred_mono_back, 4919 self._view.ui.btn_pred_mono_next, 4920 self._view.ui.lbl_pred_mono_seq_name, 4921 self._view.ui.txt_pred_mono_seq_name, 4922 self._view.ui.lbl_pred_mono_seq_name_status, 4923 self._view.ui.btn_pred_mono_back_2, 4924 self._view.ui.btn_pred_mono_add_protein, 4925 ] 4926 gui_utils.show_gui_elements(gui_elements_to_show) 4927 gui_utils.hide_gui_elements(gui_elements_to_hide) 4928 self._view.ui.btn_pred_mono_seq_to_predict_remove.setEnabled(False) 4929 self.local_pred_mono_check_if_table_is_empty() 4930 4931 def local_pred_mono_item_changed(self) -> None: 4932 """Enables the remove button.""" 4933 self._view.ui.btn_pred_mono_seq_to_predict_remove.setEnabled(True) 4934 4935 def local_pred_mono_check_if_table_is_empty(self) -> None: 4936 """Checks if the table proteins to predict is empty.""" 4937 if self._view.ui.table_pred_mono_prot_to_predict.rowCount() == 0: 4938 styles.color_button_not_ready(self._view.ui.btn_pred_mono_predict) 4939 self._view.ui.btn_pred_mono_predict.setEnabled(False) 4940 gui_elements_to_show = [ 4941 self._view.ui.lbl_pred_mono_prot_to_predict, 4942 self._view.ui.table_pred_mono_prot_to_predict, 4943 self._view.ui.btn_pred_mono_seq_to_predict, 4944 ] 4945 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4946 gui_elements_to_hide = [ 4947 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4948 self._view.ui.lbl_pred_mono_prot_name, 4949 self._view.ui.txt_pred_mono_prot_name, 4950 self._view.ui.lbl_pred_mono_prot_name_status, 4951 self._view.ui.btn_pred_mono_back, 4952 self._view.ui.btn_pred_mono_next, 4953 self._view.ui.lbl_pred_mono_seq_name, 4954 self._view.ui.txt_pred_mono_seq_name, 4955 self._view.ui.lbl_pred_mono_seq_name_status, 4956 self._view.ui.btn_pred_mono_back_2, 4957 self._view.ui.btn_pred_mono_add_protein, 4958 self._view.ui.lbl_pred_mono_advanced_config, 4959 self._view.ui.btn_pred_mono_advanced_config, 4960 self._view.ui.btn_pred_mono_predict, 4961 ] 4962 gui_utils.show_gui_elements(gui_elements_to_show) 4963 gui_utils.hide_gui_elements(gui_elements_to_hide) 4964 else: 4965 self._view.ui.btn_pred_mono_predict.setEnabled(True) 4966 4967 # </editor-fold> 4968 4969 # <editor-fold desc="Multimer local prediction"> 4970 def _init_local_pred_multi_page(self) -> None: 4971 """Clears all text boxes and sets default values for the gui elements.""" 4972 # clears everything 4973 self._view.ui.txt_pred_multi_prot_name.clear() 4974 self._view.ui.txt_pred_multi_prot_seq.clear() 4975 self._view.ui.list_pred_multi_prot_seq_overview.clear() 4976 # sets up defaults: Prediction 4977 self._view.ui.btn_pred_multi_next.setEnabled(False) 4978 self._view.ui.btn_pred_multi_prot_to_predict_add_2.setEnabled(False) 4979 self._view.ui.lbl_pred_multi_prot_name_status.setText("") 4980 self._view.ui.lbl_pred_multi_prot_seq_status.setText("") 4981 4982 def display_local_pred_multi(self) -> None: 4983 """Displays the local prediction multimer page.""" 4984 # checks internet connection 4985 if not tools.check_internet_connectivity(): 4986 gui_utils.no_internet_dialog() 4987 return 4988 4989 gui_elements_to_show = [ 4990 self._view.ui.lbl_pred_multi_prot_to_predict, 4991 self._view.ui.table_pred_multi_prot_to_predict, 4992 self._view.ui.btn_pred_multi_prot_to_predict_add, 4993 ] 4994 gui_elements_to_hide = [ 4995 self._view.ui.btn_pred_multi_prot_to_predict_remove, 4996 self._view.ui.lbl_pred_multi_prot_name_status, 4997 self._view.ui.btn_pred_multi_back, 4998 self._view.ui.btn_pred_multi_next, 4999 self._view.ui.lbl_pred_multi_prot_name, 5000 self._view.ui.txt_pred_multi_prot_name, 5001 self._view.ui.lbl_pred_multi_prot_seq, 5002 self._view.ui.txt_pred_multi_prot_seq, 5003 self._view.ui.lbl_pred_multi_prot_seq_status, 5004 self._view.ui.lbl_pred_multi_prot_seq_add, 5005 self._view.ui.btn_pred_multi_prot_seq_add, 5006 self._view.ui.lbl_pred_multi_prot_seq_overview, 5007 self._view.ui.list_pred_multi_prot_seq_overview, 5008 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5009 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5010 self._view.ui.btn_pred_multi_back_2, 5011 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5012 self._view.ui.lbl_pred_multi_advanced_config, 5013 self._view.ui.btn_pred_multi_advanced_config, 5014 self._view.ui.btn_pred_multi_predict, 5015 ] 5016 for i in range(self._view.ui.table_pred_multi_prot_to_predict.rowCount() - 1, -1, -1): 5017 self._view.ui.table_pred_multi_prot_to_predict.removeRow(i) 5018 gui_utils.show_gui_elements(gui_elements_to_show) 5019 gui_utils.hide_gui_elements(gui_elements_to_hide) 5020 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 20, "Local Multimer Prediction") 5021 self.last_sidebar_button = styles.color_sidebar_buttons( 5022 self.last_sidebar_button, 5023 self._view.ui.btn_pred_local_multimer_page, 5024 ) 5025 5026 def local_pred_multi_validate_protein_name(self) -> None: 5027 """Validates the input of the protein name in real-time.""" 5028 if safeguard.Safeguard.check_if_value_is_in_table_v_header( 5029 self._view.ui.txt_pred_multi_prot_name.text(), 5030 self._view.ui.table_pred_multi_prot_to_predict, 5031 ): 5032 self._view.ui.lbl_pred_multi_prot_name_status.setText("Protein name already used.") 5033 self._view.ui.btn_pred_multi_next.setEnabled(False) 5034 styles.color_button_not_ready(self._view.ui.btn_pred_multi_next) 5035 else: 5036 self._view.ui.btn_pred_multi_next.setEnabled(True) 5037 tools.validate_protein_name( 5038 self._view.ui.txt_pred_multi_prot_name, 5039 self._view.ui.lbl_pred_multi_prot_name_status, 5040 self._view.ui.btn_pred_multi_next, 5041 ) 5042 5043 def local_pred_multi_validate_protein_sequence(self) -> None: 5044 """Validates the input of the protein sequence in real-time.""" 5045 tools.validate_protein_sequence( 5046 self._view.ui.txt_pred_multi_prot_seq, 5047 self._view.ui.lbl_pred_multi_prot_seq_status, 5048 self._view.ui.btn_pred_multi_prot_seq_add, 5049 ) 5050 5051 def local_pred_multi_check_if_table_is_empty(self) -> None: 5052 """Checks if the table proteins to predict is empty.""" 5053 if self._view.ui.table_pred_multi_prot_to_predict.rowCount() == 0: 5054 styles.color_button_not_ready(self._view.ui.btn_pred_multi_predict) 5055 self._view.ui.btn_pred_multi_predict.setEnabled(False) 5056 gui_elements_to_show = [ 5057 self._view.ui.lbl_pred_multi_prot_to_predict, 5058 self._view.ui.table_pred_multi_prot_to_predict, 5059 self._view.ui.btn_pred_multi_prot_to_predict_add, 5060 ] 5061 gui_elements_to_hide = [ 5062 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5063 self._view.ui.lbl_pred_multi_prot_name_status, 5064 self._view.ui.btn_pred_multi_back, 5065 self._view.ui.btn_pred_multi_next, 5066 self._view.ui.lbl_pred_multi_prot_name, 5067 self._view.ui.txt_pred_multi_prot_name, 5068 self._view.ui.lbl_pred_multi_prot_seq, 5069 self._view.ui.txt_pred_multi_prot_seq, 5070 self._view.ui.lbl_pred_multi_prot_seq_status, 5071 self._view.ui.lbl_pred_multi_prot_seq_add, 5072 self._view.ui.btn_pred_multi_prot_seq_add, 5073 self._view.ui.lbl_pred_multi_prot_seq_overview, 5074 self._view.ui.list_pred_multi_prot_seq_overview, 5075 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5076 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5077 self._view.ui.btn_pred_multi_back_2, 5078 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5079 self._view.ui.lbl_pred_multi_advanced_config, 5080 self._view.ui.btn_pred_multi_advanced_config, 5081 self._view.ui.btn_pred_multi_predict, 5082 ] 5083 gui_utils.show_gui_elements(gui_elements_to_show) 5084 gui_utils.hide_gui_elements(gui_elements_to_hide) 5085 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False) 5086 else: 5087 self._view.ui.btn_pred_multi_predict.setEnabled(True) 5088 gui_elements_to_show = [ 5089 self._view.ui.lbl_pred_multi_prot_to_predict, 5090 self._view.ui.table_pred_multi_prot_to_predict, 5091 self._view.ui.btn_pred_multi_prot_to_predict_add, 5092 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5093 self._view.ui.lbl_pred_multi_advanced_config, 5094 self._view.ui.btn_pred_multi_advanced_config, 5095 self._view.ui.btn_pred_multi_predict, 5096 ] 5097 gui_elements_to_hide = [ 5098 self._view.ui.lbl_pred_multi_prot_name_status, 5099 self._view.ui.btn_pred_multi_back, 5100 self._view.ui.btn_pred_multi_next, 5101 self._view.ui.lbl_pred_multi_prot_name, 5102 self._view.ui.txt_pred_multi_prot_name, 5103 self._view.ui.lbl_pred_multi_prot_seq, 5104 self._view.ui.txt_pred_multi_prot_seq, 5105 self._view.ui.lbl_pred_multi_prot_seq_status, 5106 self._view.ui.lbl_pred_multi_prot_seq_add, 5107 self._view.ui.btn_pred_multi_prot_seq_add, 5108 self._view.ui.lbl_pred_multi_prot_seq_overview, 5109 self._view.ui.list_pred_multi_prot_seq_overview, 5110 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5111 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5112 self._view.ui.btn_pred_multi_back_2, 5113 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5114 ] 5115 gui_utils.show_gui_elements(gui_elements_to_show) 5116 gui_utils.hide_gui_elements(gui_elements_to_hide) 5117 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False) 5118 5119 def local_pred_multi_add_sequence_to_list(self) -> None: 5120 """Adds the entered sequence to the list of sequences of the protein.""" 5121 self._view.ui.list_pred_multi_prot_seq_overview.addItem( 5122 QtWidgets.QListWidgetItem(self._view.ui.txt_pred_multi_prot_seq.toPlainText()), 5123 ) 5124 self.local_pred_multi_check_if_list_is_empty() 5125 5126 def local_pred_multi_remove_sequence_to_list(self) -> None: 5127 """Removes the entered sequence to the list of sequences of the protein.""" 5128 self._view.ui.list_pred_multi_prot_seq_overview.takeItem( 5129 self._view.ui.list_pred_multi_prot_seq_overview.currentRow(), 5130 ) 5131 self.local_pred_multi_check_if_list_is_empty() 5132 self._view.ui.btn_pred_multi_prot_seq_overview_remove.setEnabled(False) 5133 5134 def local_pred_multi_check_if_list_is_empty(self) -> None: 5135 """Checks if the list of sequences of the protein is empty.""" 5136 if self._view.ui.list_pred_multi_prot_seq_overview.count() == 0: 5137 self._view.ui.btn_pred_multi_prot_to_predict_add_2.setEnabled(False) 5138 else: 5139 self._view.ui.btn_pred_multi_prot_to_predict_add_2.setEnabled(True) 5140 5141 def local_pred_multi_add(self) -> None: 5142 """Shows the gui elements for the protein name.""" 5143 gui_elements_to_show = [ 5144 self._view.ui.lbl_pred_multi_prot_to_predict, 5145 self._view.ui.table_pred_multi_prot_to_predict, 5146 self._view.ui.lbl_pred_multi_prot_name, 5147 self._view.ui.txt_pred_multi_prot_name, 5148 self._view.ui.lbl_pred_multi_prot_name_status, 5149 self._view.ui.btn_pred_multi_back, 5150 self._view.ui.btn_pred_multi_next, 5151 ] 5152 gui_elements_to_hide = [ 5153 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5154 self._view.ui.btn_pred_multi_prot_to_predict_add, 5155 self._view.ui.lbl_pred_multi_prot_seq, 5156 self._view.ui.txt_pred_multi_prot_seq, 5157 self._view.ui.lbl_pred_multi_prot_seq_status, 5158 self._view.ui.lbl_pred_multi_prot_seq_add, 5159 self._view.ui.btn_pred_multi_prot_seq_add, 5160 self._view.ui.lbl_pred_multi_prot_seq_overview, 5161 self._view.ui.list_pred_multi_prot_seq_overview, 5162 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5163 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5164 self._view.ui.btn_pred_multi_back_2, 5165 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5166 self._view.ui.lbl_pred_multi_advanced_config, 5167 self._view.ui.btn_pred_multi_advanced_config, 5168 self._view.ui.btn_pred_multi_predict, 5169 ] 5170 gui_utils.show_gui_elements(gui_elements_to_show) 5171 gui_utils.hide_gui_elements(gui_elements_to_hide) 5172 gui_utils.enable_text_box(self._view.ui.txt_pred_multi_prot_name, self._view.ui.lbl_pred_multi_prot_name) 5173 gui_utils.disable_text_box(self._view.ui.txt_pred_multi_prot_seq, self._view.ui.lbl_pred_multi_prot_seq) 5174 self._view.ui.btn_pred_multi_next.setEnabled(False) 5175 self._view.ui.txt_pred_multi_prot_name.clear() 5176 styles.color_button_not_ready(self._view.ui.btn_pred_multi_next) 5177 if self._view.ui.table_pred_multi_prot_to_predict.rowCount() > 0: 5178 try: 5179 self._view.ui.table_pred_multi_prot_to_predict.currentItem().setSelected(False) 5180 except AttributeError: 5181 constants.PYSSA_LOGGER.debug("No selection on Local Multimer Prediction in overview table.") 5182 5183 def local_pred_multi_back(self) -> None: 5184 """Hides the gui elements for the protein name.""" 5185 gui_elements_to_show = [ 5186 self._view.ui.lbl_pred_multi_prot_to_predict, 5187 self._view.ui.table_pred_multi_prot_to_predict, 5188 self._view.ui.btn_pred_multi_prot_to_predict_add, 5189 ] 5190 gui_elements_to_hide = [ 5191 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5192 self._view.ui.lbl_pred_multi_prot_name, 5193 self._view.ui.txt_pred_multi_prot_name, 5194 self._view.ui.lbl_pred_multi_prot_name_status, 5195 self._view.ui.btn_pred_multi_back, 5196 self._view.ui.btn_pred_multi_next, 5197 self._view.ui.lbl_pred_multi_prot_seq, 5198 self._view.ui.txt_pred_multi_prot_seq, 5199 self._view.ui.lbl_pred_multi_prot_seq_status, 5200 self._view.ui.lbl_pred_multi_prot_seq_add, 5201 self._view.ui.btn_pred_multi_prot_seq_add, 5202 self._view.ui.lbl_pred_multi_prot_seq_overview, 5203 self._view.ui.list_pred_multi_prot_seq_overview, 5204 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5205 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5206 self._view.ui.btn_pred_multi_back_2, 5207 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5208 self._view.ui.lbl_pred_multi_advanced_config, 5209 self._view.ui.btn_pred_multi_advanced_config, 5210 self._view.ui.btn_pred_multi_predict, 5211 ] 5212 gui_utils.show_gui_elements(gui_elements_to_show) 5213 gui_utils.hide_gui_elements(gui_elements_to_hide) 5214 self.local_pred_multi_check_if_table_is_empty() 5215 5216 def local_pred_multi_next(self) -> None: 5217 """Shows the gui elements for the protein sequence.""" 5218 gui_elements_to_show = [ 5219 self._view.ui.lbl_pred_multi_prot_to_predict, 5220 self._view.ui.table_pred_multi_prot_to_predict, 5221 self._view.ui.lbl_pred_multi_prot_name, 5222 self._view.ui.txt_pred_multi_prot_name, 5223 self._view.ui.lbl_pred_multi_prot_seq, 5224 self._view.ui.txt_pred_multi_prot_seq, 5225 self._view.ui.lbl_pred_multi_prot_seq_status, 5226 self._view.ui.lbl_pred_multi_prot_seq_add, 5227 self._view.ui.btn_pred_multi_prot_seq_add, 5228 self._view.ui.lbl_pred_multi_prot_seq_overview, 5229 self._view.ui.list_pred_multi_prot_seq_overview, 5230 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5231 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5232 self._view.ui.btn_pred_multi_back_2, 5233 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5234 ] 5235 gui_elements_to_hide = [ 5236 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5237 self._view.ui.btn_pred_multi_prot_to_predict_add, 5238 self._view.ui.lbl_pred_multi_prot_name_status, 5239 self._view.ui.btn_pred_multi_back, 5240 self._view.ui.btn_pred_multi_next, 5241 self._view.ui.lbl_pred_multi_advanced_config, 5242 self._view.ui.btn_pred_multi_advanced_config, 5243 self._view.ui.btn_pred_multi_predict, 5244 ] 5245 gui_utils.show_gui_elements(gui_elements_to_show) 5246 gui_utils.hide_gui_elements(gui_elements_to_hide) 5247 gui_utils.enable_text_box(self._view.ui.txt_pred_multi_prot_seq, self._view.ui.lbl_pred_multi_prot_seq) 5248 gui_utils.disable_text_box(self._view.ui.txt_pred_multi_prot_name, self._view.ui.lbl_pred_multi_prot_name) 5249 self._view.ui.txt_pred_multi_prot_seq.clear() 5250 self._view.ui.list_pred_multi_prot_seq_overview.clear() 5251 self._view.ui.btn_pred_multi_prot_to_predict_add_2.setEnabled(False) 5252 self._view.ui.btn_pred_multi_prot_seq_overview_remove.setEnabled(False) 5253 styles.color_button_not_ready(self._view.ui.btn_pred_multi_prot_to_predict_add_2) 5254 5255 def local_pred_multi_back_2(self) -> None: 5256 """Hides the gui elements for the protein sequence.""" 5257 gui_elements_to_show = [ 5258 self._view.ui.lbl_pred_multi_prot_to_predict, 5259 self._view.ui.table_pred_multi_prot_to_predict, 5260 self._view.ui.lbl_pred_multi_prot_name_status, 5261 self._view.ui.btn_pred_multi_back, 5262 self._view.ui.btn_pred_multi_next, 5263 self._view.ui.lbl_pred_multi_prot_name, 5264 self._view.ui.txt_pred_multi_prot_name, 5265 ] 5266 gui_elements_to_hide = [ 5267 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5268 self._view.ui.btn_pred_multi_prot_to_predict_add, 5269 self._view.ui.lbl_pred_multi_prot_seq, 5270 self._view.ui.txt_pred_multi_prot_seq, 5271 self._view.ui.lbl_pred_multi_prot_seq_status, 5272 self._view.ui.lbl_pred_multi_prot_seq_add, 5273 self._view.ui.btn_pred_multi_prot_seq_add, 5274 self._view.ui.lbl_pred_multi_prot_seq_overview, 5275 self._view.ui.list_pred_multi_prot_seq_overview, 5276 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5277 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5278 self._view.ui.btn_pred_multi_back_2, 5279 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5280 self._view.ui.lbl_pred_multi_advanced_config, 5281 self._view.ui.btn_pred_multi_advanced_config, 5282 self._view.ui.btn_pred_multi_predict, 5283 ] 5284 gui_utils.show_gui_elements(gui_elements_to_show) 5285 gui_utils.hide_gui_elements(gui_elements_to_hide) 5286 gui_utils.enable_text_box(self._view.ui.txt_pred_multi_prot_name, self._view.ui.lbl_pred_multi_prot_name) 5287 gui_utils.disable_text_box(self._view.ui.txt_pred_multi_prot_seq, self._view.ui.lbl_pred_multi_prot_seq) 5288 5289 def local_pred_multi_prot_seq_overview_item_changed(self) -> None: 5290 """Enables the remove button of the list sequences of the protein.""" 5291 self._view.ui.btn_pred_multi_prot_seq_overview_remove.setEnabled(True) 5292 5293 def local_pred_multi_prot_to_predict_item_changed(self) -> None: 5294 """Enables the remove button of the table proteins to predict.""" 5295 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(True) 5296 5297 def local_pred_multi_prot_to_predict_add_2(self) -> None: 5298 """Adds the protein to the list of proteins to predict.""" 5299 for i in range(self._view.ui.list_pred_multi_prot_seq_overview.count()): 5300 self._view.ui.table_pred_multi_prot_to_predict.setRowCount( 5301 self._view.ui.table_pred_multi_prot_to_predict.rowCount() + 1, 5302 ) 5303 self._view.ui.table_pred_multi_prot_to_predict.insertRow( 5304 self._view.ui.table_pred_multi_prot_to_predict.rowCount() + 1, 5305 ) 5306 tmp_chain_seq = ( 5307 constants.chain_dict.get(i), 5308 self._view.ui.list_pred_multi_prot_seq_overview.item(i).text(), 5309 ) 5310 self._view.ui.table_pred_multi_prot_to_predict.setItem( 5311 self._view.ui.table_pred_multi_prot_to_predict.rowCount() - 1, 5312 0, 5313 QtWidgets.QTableWidgetItem(tmp_chain_seq[0]), 5314 ) 5315 self._view.ui.table_pred_multi_prot_to_predict.setItem( 5316 self._view.ui.table_pred_multi_prot_to_predict.rowCount() - 1, 5317 1, 5318 QtWidgets.QTableWidgetItem(tmp_chain_seq[1]), 5319 ) 5320 name_item = QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_multi_prot_name.text()) 5321 self._view.ui.table_pred_multi_prot_to_predict.setVerticalHeaderItem( 5322 self._view.ui.table_pred_multi_prot_to_predict.rowCount() - 1, 5323 name_item, 5324 ) 5325 self._view.ui.table_pred_multi_prot_to_predict.resizeColumnsToContents() 5326 self.local_pred_multi_check_if_table_is_empty() 5327 gui_elements_to_show = [ 5328 self._view.ui.lbl_pred_multi_prot_to_predict, 5329 self._view.ui.table_pred_multi_prot_to_predict, 5330 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5331 self._view.ui.btn_pred_multi_prot_to_predict_add, 5332 self._view.ui.lbl_pred_multi_advanced_config, 5333 self._view.ui.btn_pred_multi_advanced_config, 5334 self._view.ui.btn_pred_multi_predict, 5335 ] 5336 gui_elements_to_hide = [ 5337 self._view.ui.lbl_pred_multi_prot_name_status, 5338 self._view.ui.btn_pred_multi_back, 5339 self._view.ui.btn_pred_multi_next, 5340 self._view.ui.lbl_pred_multi_prot_name, 5341 self._view.ui.txt_pred_multi_prot_name, 5342 self._view.ui.lbl_pred_multi_prot_seq, 5343 self._view.ui.txt_pred_multi_prot_seq, 5344 self._view.ui.lbl_pred_multi_prot_seq_status, 5345 self._view.ui.lbl_pred_multi_prot_seq_add, 5346 self._view.ui.btn_pred_multi_prot_seq_add, 5347 self._view.ui.lbl_pred_multi_prot_seq_overview, 5348 self._view.ui.list_pred_multi_prot_seq_overview, 5349 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5350 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5351 self._view.ui.btn_pred_multi_back_2, 5352 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5353 ] 5354 gui_utils.show_gui_elements(gui_elements_to_show) 5355 gui_utils.hide_gui_elements(gui_elements_to_hide) 5356 self._init_local_pred_multi_page() 5357 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False) 5358 5359 def local_pred_multi_remove(self) -> None: 5360 """Removes the selected protein from the list of proteins to predict.""" 5361 self._view.ui.table_pred_multi_prot_to_predict.removeRow( 5362 self._view.ui.table_pred_multi_prot_to_predict.currentRow(), 5363 ) 5364 if self._view.ui.table_pred_multi_prot_to_predict.rowCount() > 0: 5365 prot_name = self._view.ui.table_pred_multi_prot_to_predict.verticalHeaderItem( 5366 self._view.ui.table_pred_multi_prot_to_predict.currentRow(), 5367 ).text() 5368 for i in range(self._view.ui.table_pred_multi_prot_to_predict.rowCount()): 5369 if self._view.ui.table_pred_multi_prot_to_predict.verticalHeaderItem(i).text() == prot_name: 5370 self._view.ui.table_pred_multi_prot_to_predict.setItem( 5371 i, 5372 0, 5373 QtWidgets.QTableWidgetItem(constants.chain_dict.get(i)), 5374 ) 5375 self.local_pred_multi_check_if_table_is_empty() 5376 gui_elements_to_show = [ 5377 self._view.ui.lbl_pred_multi_prot_to_predict, 5378 self._view.ui.table_pred_multi_prot_to_predict, 5379 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5380 self._view.ui.btn_pred_multi_prot_to_predict_add, 5381 self._view.ui.lbl_pred_multi_advanced_config, 5382 self._view.ui.btn_pred_multi_advanced_config, 5383 self._view.ui.btn_pred_multi_predict, 5384 ] 5385 gui_elements_to_hide = [ 5386 self._view.ui.lbl_pred_multi_prot_name_status, 5387 self._view.ui.btn_pred_multi_back, 5388 self._view.ui.btn_pred_multi_next, 5389 self._view.ui.lbl_pred_multi_prot_name, 5390 self._view.ui.txt_pred_multi_prot_name, 5391 self._view.ui.lbl_pred_multi_prot_seq, 5392 self._view.ui.txt_pred_multi_prot_seq, 5393 self._view.ui.lbl_pred_multi_prot_seq_status, 5394 self._view.ui.lbl_pred_multi_prot_seq_add, 5395 self._view.ui.btn_pred_multi_prot_seq_add, 5396 self._view.ui.lbl_pred_multi_prot_seq_overview, 5397 self._view.ui.list_pred_multi_prot_seq_overview, 5398 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5399 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5400 self._view.ui.btn_pred_multi_back_2, 5401 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5402 ] 5403 gui_utils.show_gui_elements(gui_elements_to_show) 5404 gui_utils.hide_gui_elements(gui_elements_to_hide) 5405 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False) 5406 self.local_pred_multi_check_if_table_is_empty() 5407 5408 # </editor-fold> 5409 5410 # <editor-fold desc="Monomer prediction + analysis"> 5411 def _init_mono_pred_analysis_page(self) -> None: 5412 """Clears all text boxes and sets default values for the gui elements.""" 5413 # <editor-fold desc="Prediction section"> 5414 self._view.ui.txt_pred_analysis_mono_prot_name.clear() 5415 self._view.ui.txt_pred_analysis_mono_seq_name.clear() 5416 for i in range(self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount()): 5417 self._view.ui.table_pred_analysis_mono_prot_to_predict.removeRow(i) 5418 # sets up defaults: Prediction 5419 self._view.ui.btn_pred_analysis_mono_next.setEnabled(False) 5420 self._view.ui.btn_pred_analysis_mono_add_protein.setEnabled(False) 5421 self._view.ui.lbl_pred_analysis_mono_prot_name_status.setText("") 5422 self._view.ui.lbl_pred_analysis_mono_seq_name_status.setText("") 5423 5424 # </editor-fold> 5425 5426 # <editor-fold desc="Analysis section"> 5427 self._view.ui.list_pred_analysis_mono_overview.clear() 5428 self._view.ui.btn_pred_analysis_mono_remove.hide() 5429 5430 # </editor-fold> 5431 5432 def display_monomer_pred_analysis(self) -> None: 5433 """Displays the monomer prediction + analysis page.""" 5434 # checks internet connection 5435 if not tools.check_internet_connectivity(): 5436 gui_utils.no_internet_dialog() 5437 return 5438 5439 self._init_mono_pred_analysis_page() 5440 self._view.ui.table_pred_analysis_mono_prot_to_predict.clear() 5441 self._view.ui.table_pred_analysis_mono_prot_to_predict.setHorizontalHeaderItem( 5442 0, 5443 QtWidgets.QTableWidgetItem("Chain"), 5444 ) 5445 self._view.ui.table_pred_analysis_mono_prot_to_predict.setHorizontalHeaderItem( 5446 1, 5447 QtWidgets.QTableWidgetItem("Sequence"), 5448 ) 5449 self._view.ui.table_pred_analysis_mono_prot_to_predict.resizeColumnsToContents() 5450 gui_elements_to_show = [ 5451 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5452 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5453 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5454 ] 5455 gui_elements_to_hide = [ 5456 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5457 self._view.ui.lbl_pred_analysis_mono_prot_name, 5458 self._view.ui.txt_pred_analysis_mono_prot_name, 5459 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5460 self._view.ui.btn_pred_analysis_mono_back, 5461 self._view.ui.btn_pred_analysis_mono_next, 5462 self._view.ui.lbl_pred_analysis_mono_seq_name, 5463 self._view.ui.txt_pred_analysis_mono_seq_name, 5464 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5465 self._view.ui.btn_pred_analysis_mono_back_2, 5466 self._view.ui.btn_pred_analysis_mono_add_protein, 5467 self._view.ui.lbl_pred_mono_advanced_config_2, 5468 self._view.ui.btn_pred_mono_advanced_config_2, 5469 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5470 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5471 ] 5472 gui_utils.show_gui_elements(gui_elements_to_show) 5473 gui_utils.hide_gui_elements(gui_elements_to_hide) 5474 if self._view.ui.tabWidget.currentIndex() == 1: 5475 self._view.ui.tabWidget.setCurrentIndex(0) 5476 self._view.ui.tabWidget.setTabEnabled(1, False) 5477 self._view.ui.tabWidget.setTabEnabled(0, True) 5478 tools.switch_page( 5479 self._view.ui.stackedWidget, 5480 self._view.ui.lbl_page_title, 5481 21, 5482 "Monomer Prediction + Analysis", 5483 ) 5484 self.last_sidebar_button = styles.color_sidebar_buttons( 5485 self.last_sidebar_button, 5486 self._view.ui.btn_pred_analysis_monomer_page, 5487 ) 5488 self._view.ui.table_pred_analysis_mono_prot_to_predict.setEnabled(True) 5489 5490 # <editor-fold desc="Sections"> 5491 5492 # <editor-fold desc="Prediction section"> 5493 def mono_pred_analysis_validate_protein_name(self) -> None: 5494 """Validates the input of the protein name in real-time.""" 5495 if safeguard.Safeguard.check_if_value_is_in_table_v_header( 5496 self._view.ui.txt_pred_analysis_mono_prot_name.text(), 5497 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5498 ): 5499 self._view.ui.lbl_pred_analysis_mono_prot_name_status.setText("Protein name already used.") 5500 self._view.ui.btn_pred_analysis_mono_next.setEnabled(False) 5501 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_mono_next) 5502 else: 5503 self._view.ui.btn_pred_analysis_mono_next.setEnabled(True) 5504 tools.validate_protein_name( 5505 self._view.ui.txt_pred_analysis_mono_prot_name, 5506 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5507 self._view.ui.btn_pred_analysis_mono_next, 5508 ) 5509 5510 def mono_pred_analysis_validate_protein_sequence(self) -> None: 5511 """Validates the input of the protein sequence in real-time.""" 5512 tools.validate_protein_sequence( 5513 self._view.ui.txt_pred_analysis_mono_seq_name, 5514 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5515 self._view.ui.btn_pred_analysis_mono_add_protein, 5516 ) 5517 5518 def mono_pred_analysis_check_if_table_is_empty(self) -> None: 5519 """Checks if the table proteins to predict is empty.""" 5520 if self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() == 0: 5521 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_mono_go_analysis_setup) 5522 self._view.ui.btn_pred_analysis_mono_go_analysis_setup.setEnabled(False) 5523 gui_elements_to_show = [ 5524 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5525 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5526 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5527 ] 5528 gui_elements_to_hide = [ 5529 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5530 self._view.ui.lbl_pred_analysis_mono_prot_name, 5531 self._view.ui.txt_pred_analysis_mono_prot_name, 5532 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5533 self._view.ui.btn_pred_analysis_mono_back, 5534 self._view.ui.btn_pred_analysis_mono_next, 5535 self._view.ui.lbl_pred_analysis_mono_seq_name, 5536 self._view.ui.txt_pred_analysis_mono_seq_name, 5537 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5538 self._view.ui.btn_pred_analysis_mono_back_2, 5539 self._view.ui.btn_pred_analysis_mono_add_protein, 5540 self._view.ui.lbl_pred_mono_advanced_config_2, 5541 self._view.ui.btn_pred_mono_advanced_config_2, 5542 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5543 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5544 ] 5545 gui_utils.show_gui_elements(gui_elements_to_show) 5546 gui_utils.hide_gui_elements(gui_elements_to_hide) 5547 else: 5548 gui_elements_to_show = [ 5549 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5550 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5551 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5552 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5553 self._view.ui.lbl_pred_mono_advanced_config_2, 5554 self._view.ui.btn_pred_mono_advanced_config_2, 5555 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5556 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5557 ] 5558 gui_elements_to_hide = [ 5559 self._view.ui.lbl_pred_analysis_mono_prot_name, 5560 self._view.ui.txt_pred_analysis_mono_prot_name, 5561 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5562 self._view.ui.btn_pred_analysis_mono_back, 5563 self._view.ui.btn_pred_analysis_mono_next, 5564 self._view.ui.lbl_pred_analysis_mono_seq_name, 5565 self._view.ui.txt_pred_analysis_mono_seq_name, 5566 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5567 self._view.ui.btn_pred_analysis_mono_back_2, 5568 self._view.ui.btn_pred_analysis_mono_add_protein, 5569 ] 5570 gui_utils.show_gui_elements(gui_elements_to_show) 5571 gui_utils.hide_gui_elements(gui_elements_to_hide) 5572 self._view.ui.btn_pred_analysis_mono_go_analysis_setup.setEnabled(True) 5573 5574 def setup_defaults_monomer_prediction_analysis(self) -> None: 5575 """Sets up default values for the prediction tab.""" 5576 # clears everything 5577 self._view.ui.txt_pred_analysis_mono_prot_name.clear() 5578 self._view.ui.txt_pred_analysis_mono_seq_name.clear() 5579 # sets up defaults: Prediction 5580 self._view.ui.btn_pred_analysis_mono_next.setEnabled(False) 5581 self._view.ui.btn_pred_analysis_mono_add_protein.setEnabled(False) 5582 self._view.ui.lbl_pred_analysis_mono_prot_name_status.setText("") 5583 self._view.ui.lbl_pred_analysis_mono_seq_name_status.setText("") 5584 5585 def mono_pred_analysis_add_seq_to_predict(self) -> None: 5586 """Shows the gui elements for the protein name.""" 5587 gui_elements_to_show = [ 5588 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5589 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5590 self._view.ui.lbl_pred_analysis_mono_prot_name, 5591 self._view.ui.txt_pred_analysis_mono_prot_name, 5592 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5593 self._view.ui.btn_pred_analysis_mono_back, 5594 self._view.ui.btn_pred_analysis_mono_next, 5595 ] 5596 gui_utils.enable_text_box( 5597 self._view.ui.txt_pred_analysis_mono_prot_name, 5598 self._view.ui.lbl_pred_analysis_mono_prot_name, 5599 ) 5600 gui_elements_to_hide = [ 5601 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5602 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5603 self._view.ui.lbl_pred_analysis_mono_seq_name, 5604 self._view.ui.txt_pred_analysis_mono_seq_name, 5605 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5606 self._view.ui.btn_pred_analysis_mono_back_2, 5607 self._view.ui.btn_pred_analysis_mono_add_protein, 5608 self._view.ui.lbl_pred_mono_advanced_config_2, 5609 self._view.ui.btn_pred_mono_advanced_config_2, 5610 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5611 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5612 ] 5613 gui_utils.disable_text_box( 5614 self._view.ui.txt_pred_analysis_mono_seq_name, 5615 self._view.ui.lbl_pred_analysis_mono_seq_name, 5616 ) 5617 gui_utils.show_gui_elements(gui_elements_to_show) 5618 gui_utils.hide_gui_elements(gui_elements_to_hide) 5619 self._view.ui.btn_pred_analysis_mono_next.setEnabled(False) 5620 self._view.ui.txt_pred_analysis_mono_prot_name.clear() 5621 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_mono_next) 5622 if self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() > 0: 5623 try: 5624 self._view.ui.table_pred_analysis_mono_prot_to_predict.currentItem().setSelected(False) 5625 except AttributeError: 5626 constants.PYSSA_LOGGER.debug("No selection on Local Monomer Prediction in overview table.") 5627 5628 def mono_pred_analysis_back(self) -> None: 5629 """Hides the gui elements for the protein name.""" 5630 gui_elements_to_show = [ 5631 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5632 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5633 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5634 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5635 ] 5636 gui_elements_to_hide = [ 5637 self._view.ui.lbl_pred_analysis_mono_prot_name, 5638 self._view.ui.txt_pred_analysis_mono_prot_name, 5639 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5640 self._view.ui.btn_pred_analysis_mono_back, 5641 self._view.ui.btn_pred_analysis_mono_next, 5642 self._view.ui.lbl_pred_analysis_mono_seq_name, 5643 self._view.ui.txt_pred_analysis_mono_seq_name, 5644 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5645 self._view.ui.btn_pred_analysis_mono_back_2, 5646 self._view.ui.btn_pred_analysis_mono_add_protein, 5647 self._view.ui.lbl_pred_mono_advanced_config_2, 5648 self._view.ui.btn_pred_mono_advanced_config_2, 5649 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5650 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5651 ] 5652 gui_utils.show_gui_elements(gui_elements_to_show) 5653 gui_utils.hide_gui_elements(gui_elements_to_hide) 5654 self.mono_pred_analysis_check_if_table_is_empty() 5655 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.setEnabled(False) 5656 5657 def mono_pred_analysis_next(self) -> None: 5658 """Shows the gui elements for the protein sequence.""" 5659 gui_elements_to_show = [ 5660 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5661 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5662 self._view.ui.lbl_pred_analysis_mono_prot_name, 5663 self._view.ui.txt_pred_analysis_mono_prot_name, 5664 self._view.ui.lbl_pred_analysis_mono_seq_name, 5665 self._view.ui.txt_pred_analysis_mono_seq_name, 5666 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5667 self._view.ui.btn_pred_analysis_mono_back_2, 5668 self._view.ui.btn_pred_analysis_mono_add_protein, 5669 ] 5670 gui_utils.enable_text_box( 5671 self._view.ui.txt_pred_analysis_mono_seq_name, 5672 self._view.ui.lbl_pred_analysis_mono_seq_name, 5673 ) 5674 gui_elements_to_hide = [ 5675 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5676 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5677 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5678 self._view.ui.btn_pred_analysis_mono_back, 5679 self._view.ui.btn_pred_analysis_mono_next, 5680 self._view.ui.lbl_pred_mono_advanced_config_2, 5681 self._view.ui.btn_pred_mono_advanced_config_2, 5682 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5683 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5684 ] 5685 gui_utils.disable_text_box( 5686 self._view.ui.txt_pred_analysis_mono_prot_name, 5687 self._view.ui.lbl_pred_analysis_mono_prot_name, 5688 ) 5689 gui_utils.show_gui_elements(gui_elements_to_show) 5690 gui_utils.hide_gui_elements(gui_elements_to_hide) 5691 self._view.ui.txt_pred_analysis_mono_seq_name.clear() 5692 5693 def mono_pred_analysis_back_2(self) -> None: 5694 """Hides the gui elements for the protein sequence.""" 5695 gui_elements_to_show = [ 5696 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5697 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5698 self._view.ui.lbl_pred_analysis_mono_prot_name, 5699 self._view.ui.txt_pred_analysis_mono_prot_name, 5700 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5701 self._view.ui.btn_pred_analysis_mono_back, 5702 self._view.ui.btn_pred_analysis_mono_next, 5703 ] 5704 gui_elements_to_hide = [ 5705 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5706 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5707 self._view.ui.lbl_pred_analysis_mono_seq_name, 5708 self._view.ui.txt_pred_analysis_mono_seq_name, 5709 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5710 self._view.ui.btn_pred_analysis_mono_back_2, 5711 self._view.ui.btn_pred_analysis_mono_add_protein, 5712 self._view.ui.lbl_pred_mono_advanced_config_2, 5713 self._view.ui.btn_pred_mono_advanced_config_2, 5714 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5715 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5716 ] 5717 gui_utils.enable_text_box( 5718 self._view.ui.txt_pred_analysis_mono_prot_name, 5719 self._view.ui.lbl_pred_analysis_mono_prot_name, 5720 ) 5721 gui_utils.disable_text_box( 5722 self._view.ui.txt_pred_analysis_mono_seq_name, 5723 self._view.ui.lbl_pred_analysis_mono_seq_name, 5724 ) 5725 gui_utils.show_gui_elements(gui_elements_to_show) 5726 gui_utils.hide_gui_elements(gui_elements_to_hide) 5727 5728 def mono_pred_analysis_add_protein(self) -> None: 5729 """Adds the protein to the list of proteins to predict.""" 5730 self._view.ui.table_pred_analysis_mono_prot_to_predict.setRowCount( 5731 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() + 1, 5732 ) 5733 self._view.ui.table_pred_analysis_mono_prot_to_predict.insertRow( 5734 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() + 1, 5735 ) 5736 self._view.ui.table_pred_analysis_mono_prot_to_predict.setItem( 5737 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5738 0, 5739 QtWidgets.QTableWidgetItem("A"), 5740 ) 5741 self._view.ui.table_pred_analysis_mono_prot_to_predict.setItem( 5742 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5743 1, 5744 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_analysis_mono_seq_name.toPlainText()), 5745 ) 5746 self._view.ui.table_pred_analysis_mono_prot_to_predict.setVerticalHeaderItem( 5747 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5748 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_analysis_mono_prot_name.text()), 5749 ) 5750 self._view.ui.table_pred_analysis_mono_prot_to_predict.resizeColumnsToContents() 5751 self.mono_pred_analysis_check_if_table_is_empty() 5752 gui_elements_to_show = [ 5753 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5754 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5755 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5756 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5757 self._view.ui.lbl_pred_mono_advanced_config_2, 5758 self._view.ui.btn_pred_mono_advanced_config_2, 5759 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5760 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5761 ] 5762 gui_utils.enable_text_box( 5763 self._view.ui.txt_pred_analysis_mono_prot_name, 5764 self._view.ui.lbl_pred_analysis_mono_prot_name, 5765 ) 5766 gui_elements_to_hide = [ 5767 self._view.ui.lbl_pred_analysis_mono_prot_name, 5768 self._view.ui.txt_pred_analysis_mono_prot_name, 5769 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5770 self._view.ui.btn_pred_analysis_mono_back, 5771 self._view.ui.btn_pred_analysis_mono_next, 5772 self._view.ui.lbl_pred_analysis_mono_seq_name, 5773 self._view.ui.txt_pred_analysis_mono_seq_name, 5774 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5775 self._view.ui.btn_pred_analysis_mono_back_2, 5776 self._view.ui.btn_pred_analysis_mono_add_protein, 5777 ] 5778 gui_utils.show_gui_elements(gui_elements_to_show) 5779 gui_utils.hide_gui_elements(gui_elements_to_hide) 5780 self._view.ui.btn_pred_analysis_mono_go_analysis_setup.setEnabled(True) 5781 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.setEnabled(False) 5782 self.setup_defaults_monomer_prediction() 5783 5784 def mono_pred_analysis_prediction_overview_item_clicked(self) -> None: 5785 """Enables the remove button.""" 5786 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.setEnabled(True) 5787 5788 def mono_pred_analysis_add_protein_to_predict(self) -> None: 5789 """Needs to be removed.""" 5790 self._view.ui.table_pred_analysis_mono_prot_to_predict.setRowCount( 5791 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() + 1, 5792 ) 5793 self._view.ui.table_pred_analysis_mono_prot_to_predict.insertRow( 5794 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() + 1, 5795 ) 5796 self._view.ui.table_pred_analysis_mono_prot_to_predict.setItem( 5797 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5798 0, 5799 QtWidgets.QTableWidgetItem("A"), 5800 ) 5801 self._view.ui.table_pred_analysis_mono_prot_to_predict.setItem( 5802 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5803 1, 5804 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_analysis_mono_seq_name.toPlainText()), 5805 ) 5806 self._view.ui.table_pred_analysis_mono_prot_to_predict.setVerticalHeaderItem( 5807 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5808 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_analysis_mono_prot_name.text()), 5809 ) 5810 self._view.ui.table_pred_analysis_mono_prot_to_predict.resizeColumnsToContents() 5811 self.mono_pred_analysis_check_if_table_is_empty() 5812 self.setup_defaults_monomer_prediction_analysis() 5813 5814 def mono_pred_analysis_remove_protein_to_predict(self) -> None: 5815 """Removes the selected protein from the list of proteins to predict.""" 5816 self._view.ui.table_pred_analysis_mono_prot_to_predict.removeRow( 5817 self._view.ui.table_pred_analysis_mono_prot_to_predict.currentRow(), 5818 ) 5819 self.mono_pred_analysis_check_if_table_is_empty() 5820 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.setEnabled(False) 5821 5822 # </editor-fold> 5823 5824 # <editor-fold desc="Analysis section"> 5825 def mono_pred_analysis_structure_analysis_add(self) -> None: 5826 """Shows the gui elements for the selection of the two proteins.""" 5827 gui_elements_to_show = [ 5828 self._view.ui.lbl_pred_analysis_mono_overview, 5829 self._view.ui.list_pred_analysis_mono_overview, 5830 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 5831 self._view.ui.box_pred_analysis_mono_prot_struct_1, 5832 self._view.ui.lbl_analysis_batch_vs_2, 5833 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 5834 self._view.ui.box_pred_analysis_mono_prot_struct_2, 5835 self._view.ui.btn_pred_analysis_mono_back_3, 5836 self._view.ui.btn_pred_analysis_mono_next_2, 5837 ] 5838 gui_elements_to_hide = [ 5839 self._view.ui.btn_pred_analysis_mono_remove, 5840 self._view.ui.btn_pred_analysis_mono_add, 5841 self._view.ui.lbl_pred_analysis_mono_ref_chains, 5842 self._view.ui.list_pred_analysis_mono_ref_chains, 5843 self._view.ui.btn_pred_analysis_mono_back_4, 5844 self._view.ui.btn_pred_analysis_mono_next_3, 5845 self._view.ui.lbl_pred_analysis_mono_model_chains, 5846 self._view.ui.list_pred_analysis_mono_model_chains, 5847 self._view.ui.btn_pred_analysis_mono_back_5, 5848 self._view.ui.btn_pred_analysis_mono_next_4, 5849 self._view.ui.lbl_pred_analysis_mono_images, 5850 self._view.ui.cb_pred_analysis_mono_images, 5851 self._view.ui.btn_pred_analysis_mono_start, 5852 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 5853 ] 5854 gui_utils.show_gui_elements(gui_elements_to_show) 5855 gui_utils.hide_gui_elements(gui_elements_to_hide) 5856 self._view.ui.lbl_pred_analysis_mono_prot_struct_1.clear() 5857 self._view.ui.lbl_pred_analysis_mono_prot_struct_2.clear() 5858 self._view.ui.lbl_pred_analysis_mono_prot_struct_1.setText("Protein structure 1") 5859 self._view.ui.lbl_pred_analysis_mono_prot_struct_2.setText("Protein structure 2") 5860 self.fill_mono_pred_analysis_protein_boxes() 5861 if self._view.ui.list_pred_analysis_mono_overview.count() > 0: 5862 try: 5863 self._view.ui.list_pred_analysis_mono_overview.currentItem().setSelected(False) 5864 except AttributeError: 5865 constants.PYSSA_LOGGER.debug("No selection in struction analysis overview.") 5866 5867 def mono_pred_analysis_structure_analysis_back_3(self) -> None: 5868 """Hides the gui elements to select the two proteins.""" 5869 gui_elements_to_show = [ 5870 self._view.ui.lbl_pred_analysis_mono_overview, 5871 self._view.ui.list_pred_analysis_mono_overview, 5872 self._view.ui.btn_pred_analysis_mono_add, 5873 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 5874 ] 5875 gui_elements_to_hide = [ 5876 self._view.ui.btn_pred_analysis_mono_remove, 5877 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 5878 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 5879 self._view.ui.lbl_analysis_batch_vs_2, 5880 self._view.ui.lbl_pred_analysis_mono_ref_chains, 5881 self._view.ui.list_pred_analysis_mono_ref_chains, 5882 self._view.ui.btn_pred_analysis_mono_back_4, 5883 self._view.ui.btn_pred_analysis_mono_next_3, 5884 self._view.ui.box_pred_analysis_mono_prot_struct_1, 5885 self._view.ui.box_pred_analysis_mono_prot_struct_2, 5886 self._view.ui.btn_pred_analysis_mono_back_3, 5887 self._view.ui.btn_pred_analysis_mono_next_2, 5888 self._view.ui.lbl_pred_analysis_mono_model_chains, 5889 self._view.ui.list_pred_analysis_mono_model_chains, 5890 self._view.ui.btn_pred_analysis_mono_back_5, 5891 self._view.ui.btn_pred_analysis_mono_next_4, 5892 self._view.ui.lbl_pred_analysis_mono_images, 5893 self._view.ui.cb_pred_analysis_mono_images, 5894 self._view.ui.btn_pred_analysis_mono_start, 5895 ] 5896 gui_utils.show_gui_elements(gui_elements_to_show) 5897 gui_utils.hide_gui_elements(gui_elements_to_hide) 5898 if self._view.ui.list_pred_analysis_mono_overview.count() > 0: 5899 self._view.ui.btn_pred_analysis_mono_remove.show() 5900 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(False) 5901 self._view.ui.btn_pred_analysis_mono_start.show() 5902 self._view.ui.lbl_pred_analysis_mono_images.show() 5903 self._view.ui.cb_pred_analysis_mono_images.show() 5904 5905 def mono_pred_analysis_structure_analysis_next_3(self) -> None: 5906 """Shows the gui elements to select the chains of protein 2.""" 5907 gui_elements_to_show = [ 5908 self._view.ui.lbl_pred_analysis_mono_overview, 5909 self._view.ui.list_pred_analysis_mono_overview, 5910 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 5911 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 5912 self._view.ui.lbl_analysis_batch_vs_2, 5913 self._view.ui.lbl_pred_analysis_mono_ref_chains, 5914 self._view.ui.list_pred_analysis_mono_ref_chains, 5915 self._view.ui.lbl_pred_analysis_mono_model_chains, 5916 self._view.ui.list_pred_analysis_mono_model_chains, 5917 self._view.ui.btn_pred_analysis_mono_back_5, 5918 self._view.ui.btn_pred_analysis_mono_next_4, 5919 ] 5920 gui_elements_to_hide = [ 5921 self._view.ui.btn_pred_analysis_mono_remove, 5922 self._view.ui.btn_pred_analysis_mono_add, 5923 self._view.ui.box_pred_analysis_mono_prot_struct_1, 5924 self._view.ui.box_pred_analysis_mono_prot_struct_2, 5925 self._view.ui.btn_pred_analysis_mono_back_3, 5926 self._view.ui.btn_pred_analysis_mono_next_2, 5927 self._view.ui.btn_pred_analysis_mono_back_4, 5928 self._view.ui.btn_pred_analysis_mono_next_3, 5929 self._view.ui.lbl_pred_analysis_mono_images, 5930 self._view.ui.cb_pred_analysis_mono_images, 5931 self._view.ui.btn_pred_analysis_mono_start, 5932 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 5933 ] 5934 gui_utils.show_gui_elements(gui_elements_to_show) 5935 gui_utils.hide_gui_elements(gui_elements_to_hide) 5936 self._view.ui.list_pred_analysis_mono_model_chains.clear() 5937 self._view.ui.list_pred_analysis_mono_ref_chains.setEnabled(False) 5938 self._view.ui.btn_pred_analysis_mono_next_4.setEnabled(False) 5939 5940 for i in range(self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount()): 5941 if ( 5942 self._view.ui.table_pred_analysis_mono_prot_to_predict.verticalHeaderItem(i).text() 5943 == self._view.ui.box_pred_analysis_mono_prot_struct_2.currentText() 5944 ): 5945 self._view.ui.list_pred_analysis_mono_model_chains.addItem( 5946 self._view.ui.table_pred_analysis_mono_prot_to_predict.item(i, 0).text(), 5947 ) 5948 if self._view.ui.list_pred_analysis_mono_model_chains.count() == 0: 5949 tmp_protein = self._current_project.search_protein( 5950 self._view.ui.box_pred_analysis_mono_prot_struct_2.currentText(), 5951 ) 5952 for tmp_chain in tmp_protein.chains: 5953 if tmp_chain.chain_type == "protein_chain": 5954 self._view.ui.list_pred_analysis_mono_model_chains.addItem(tmp_chain.chain_letter) 5955 if self._view.ui.list_pred_analysis_mono_model_chains.count() == 1: 5956 self._view.ui.lbl_pred_analysis_mono_model_chains.setText( 5957 f"Select chain in protein structure {self._view.ui.lbl_pred_analysis_mono_prot_struct_2.text()}.", 5958 ) 5959 else: 5960 self._view.ui.lbl_pred_analysis_mono_model_chains.setText( 5961 f"Select {len(self._view.ui.list_pred_analysis_mono_model_chains.selectedItems())} chains " 5962 f"in protein structure {self._view.ui.lbl_pred_analysis_mono_prot_struct_2.text()}.", 5963 ) 5964 5965 def mono_pred_analysis_structure_analysis_back_4(self) -> None: 5966 """Hides the gui elements to select the chains in protein 1.""" 5967 gui_elements_to_show = [ 5968 self._view.ui.lbl_pred_analysis_mono_overview, 5969 self._view.ui.list_pred_analysis_mono_overview, 5970 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 5971 self._view.ui.box_pred_analysis_mono_prot_struct_1, 5972 self._view.ui.lbl_analysis_batch_vs_2, 5973 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 5974 self._view.ui.box_pred_analysis_mono_prot_struct_2, 5975 self._view.ui.btn_pred_analysis_mono_back_3, 5976 self._view.ui.btn_pred_analysis_mono_next_2, 5977 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 5978 ] 5979 gui_elements_to_hide = [ 5980 self._view.ui.btn_pred_analysis_mono_remove, 5981 self._view.ui.btn_pred_analysis_mono_add, 5982 self._view.ui.lbl_pred_analysis_mono_ref_chains, 5983 self._view.ui.list_pred_analysis_mono_ref_chains, 5984 self._view.ui.btn_pred_analysis_mono_back_4, 5985 self._view.ui.btn_pred_analysis_mono_next_3, 5986 self._view.ui.lbl_pred_analysis_mono_model_chains, 5987 self._view.ui.list_pred_analysis_mono_model_chains, 5988 self._view.ui.btn_pred_analysis_mono_back_5, 5989 self._view.ui.btn_pred_analysis_mono_next_4, 5990 self._view.ui.lbl_pred_analysis_mono_images, 5991 self._view.ui.cb_pred_analysis_mono_images, 5992 self._view.ui.btn_pred_analysis_mono_start, 5993 ] 5994 gui_utils.show_gui_elements(gui_elements_to_show) 5995 gui_utils.hide_gui_elements(gui_elements_to_hide) 5996 self._view.ui.lbl_pred_analysis_mono_prot_struct_1.setText("Protein structure 1") 5997 self._view.ui.lbl_pred_analysis_mono_prot_struct_2.setText("Protein structure 2") 5998 5999 def mono_pred_analysis_structure_analysis_next_4(self) -> None: 6000 """Adds the protein pair to the list of protein pairs to analyze.""" 6001 gui_elements_to_show = [ 6002 self._view.ui.btn_pred_analysis_mono_remove, 6003 self._view.ui.btn_pred_analysis_mono_add, 6004 self._view.ui.lbl_pred_analysis_mono_overview, 6005 self._view.ui.list_pred_analysis_mono_overview, 6006 self._view.ui.lbl_pred_analysis_mono_images, 6007 self._view.ui.cb_pred_analysis_mono_images, 6008 self._view.ui.btn_pred_analysis_mono_start, 6009 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 6010 ] 6011 gui_elements_to_hide = [ 6012 self._view.ui.box_pred_analysis_mono_prot_struct_1, 6013 self._view.ui.box_pred_analysis_mono_prot_struct_2, 6014 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 6015 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 6016 self._view.ui.lbl_analysis_batch_vs_2, 6017 self._view.ui.lbl_pred_analysis_mono_ref_chains, 6018 self._view.ui.list_pred_analysis_mono_ref_chains, 6019 self._view.ui.lbl_pred_analysis_mono_model_chains, 6020 self._view.ui.list_pred_analysis_mono_model_chains, 6021 self._view.ui.btn_pred_analysis_mono_back_3, 6022 self._view.ui.btn_pred_analysis_mono_next_2, 6023 self._view.ui.btn_pred_analysis_mono_back_4, 6024 self._view.ui.btn_pred_analysis_mono_next_3, 6025 self._view.ui.btn_pred_analysis_mono_back_5, 6026 self._view.ui.btn_pred_analysis_mono_next_4, 6027 ] 6028 gui_utils.show_gui_elements(gui_elements_to_show) 6029 gui_utils.hide_gui_elements(gui_elements_to_hide) 6030 prot_1_name = self._view.ui.lbl_pred_analysis_mono_prot_struct_1.text() 6031 prot_1_chains = [] 6032 for chain in self._view.ui.list_pred_analysis_mono_ref_chains.selectedItems(): 6033 prot_1_chains.append(chain.text()) 6034 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 6035 prot_2_name = self._view.ui.lbl_pred_analysis_mono_prot_struct_2.text() 6036 prot_2_chains = [] 6037 for chain in self._view.ui.list_pred_analysis_mono_model_chains.selectedItems(): 6038 prot_2_chains.append(chain.text()) 6039 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 6040 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 6041 item = QtWidgets.QListWidgetItem(analysis_name) 6042 self._view.ui.list_pred_analysis_mono_overview.addItem(item) 6043 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(False) 6044 6045 def mono_pred_analysis_structure_analysis_back_5(self) -> None: 6046 """Hides the gui elements to select the chains in protein 2.""" 6047 gui_elements_to_show = [ 6048 self._view.ui.lbl_pred_analysis_mono_overview, 6049 self._view.ui.list_pred_analysis_mono_overview, 6050 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 6051 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 6052 self._view.ui.lbl_analysis_batch_vs_2, 6053 self._view.ui.lbl_pred_analysis_mono_ref_chains, 6054 self._view.ui.list_pred_analysis_mono_ref_chains, 6055 self._view.ui.btn_pred_analysis_mono_back_4, 6056 self._view.ui.btn_pred_analysis_mono_next_3, 6057 ] 6058 gui_elements_to_hide = [ 6059 self._view.ui.btn_pred_analysis_mono_remove, 6060 self._view.ui.btn_pred_analysis_mono_add, 6061 self._view.ui.box_pred_analysis_mono_prot_struct_1, 6062 self._view.ui.box_pred_analysis_mono_prot_struct_2, 6063 self._view.ui.btn_pred_analysis_mono_back_3, 6064 self._view.ui.btn_pred_analysis_mono_next_2, 6065 self._view.ui.btn_pred_analysis_mono_back_5, 6066 self._view.ui.btn_pred_analysis_mono_next_4, 6067 self._view.ui.lbl_pred_analysis_mono_images, 6068 self._view.ui.cb_pred_analysis_mono_images, 6069 self._view.ui.btn_pred_analysis_mono_start, 6070 self._view.ui.lbl_pred_analysis_mono_model_chains, 6071 self._view.ui.list_pred_analysis_mono_model_chains, 6072 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 6073 ] 6074 gui_utils.show_gui_elements(gui_elements_to_show) 6075 gui_utils.hide_gui_elements(gui_elements_to_hide) 6076 self._view.ui.list_pred_analysis_mono_ref_chains.setEnabled(True) 6077 6078 # tmp_protein = self._current_project.search_protein(self._view.ui.box_pred_analysis_mono_prot_struct_2.currentText()) 6079 # for tmp_chain in tmp_protein.chains: 6080 # if tmp_chain.chain_type == "protein_chain": 6081 # self._view.ui.list_pred_analysis_mono_ref_chains.addItem(tmp_chain.chain_letter) 6082 6083 def mono_pred_analysis_structure_analysis_overview_clicked(self) -> None: 6084 """Enables the remove button.""" 6085 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(True) 6086 6087 def fill_mono_pred_analysis_protein_boxes(self) -> None: 6088 """Fills the combo box of the protein structures.""" 6089 protein_names = [] 6090 for i in range(self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount()): 6091 protein_names.append(self._view.ui.table_pred_analysis_mono_prot_to_predict.verticalHeaderItem(i).text()) 6092 for tmp_protein in self._current_project.proteins: 6093 protein_names.append(tmp_protein.get_molecule_object()) 6094 protein_names.insert(0, "") 6095 self._view.ui.box_pred_analysis_mono_prot_struct_1.clear() 6096 self._view.ui.box_pred_analysis_mono_prot_struct_2.clear() 6097 gui_utils.fill_combo_box(self._view.ui.box_pred_analysis_mono_prot_struct_1, protein_names) 6098 gui_utils.fill_combo_box(self._view.ui.box_pred_analysis_mono_prot_struct_2, protein_names) 6099 6100 def remove_mono_pred_analysis_analysis_run(self) -> None: 6101 """Removes a selected protein pair form the list of protein pairs to analyze.""" 6102 self._view.ui.list_pred_analysis_mono_overview.takeItem( 6103 self._view.ui.list_pred_analysis_mono_overview.currentRow(), 6104 ) 6105 gui_elements_to_show = [ 6106 self._view.ui.lbl_pred_analysis_mono_overview, 6107 self._view.ui.list_pred_analysis_mono_overview, 6108 self._view.ui.btn_pred_analysis_mono_add, 6109 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 6110 ] 6111 gui_elements_to_hide = [ 6112 self._view.ui.btn_pred_analysis_mono_remove, 6113 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 6114 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 6115 self._view.ui.lbl_analysis_batch_vs_2, 6116 self._view.ui.lbl_pred_analysis_mono_ref_chains, 6117 self._view.ui.list_pred_analysis_mono_ref_chains, 6118 self._view.ui.btn_pred_analysis_mono_back_4, 6119 self._view.ui.btn_pred_analysis_mono_next_3, 6120 self._view.ui.box_pred_analysis_mono_prot_struct_1, 6121 self._view.ui.box_pred_analysis_mono_prot_struct_2, 6122 self._view.ui.btn_pred_analysis_mono_back_3, 6123 self._view.ui.btn_pred_analysis_mono_next_2, 6124 self._view.ui.lbl_pred_analysis_mono_model_chains, 6125 self._view.ui.list_pred_analysis_mono_model_chains, 6126 self._view.ui.btn_pred_analysis_mono_back_5, 6127 self._view.ui.btn_pred_analysis_mono_next_4, 6128 self._view.ui.lbl_pred_analysis_mono_images, 6129 self._view.ui.cb_pred_analysis_mono_images, 6130 self._view.ui.btn_pred_analysis_mono_start, 6131 ] 6132 gui_utils.show_gui_elements(gui_elements_to_show) 6133 gui_utils.hide_gui_elements(gui_elements_to_hide) 6134 if self._view.ui.list_pred_analysis_mono_overview.count() > 0: 6135 self._view.ui.btn_pred_analysis_mono_remove.show() 6136 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(False) 6137 self._view.ui.btn_pred_analysis_mono_start.show() 6138 self._view.ui.lbl_pred_analysis_mono_images.show() 6139 self._view.ui.cb_pred_analysis_mono_images.show() 6140 # if self._view.ui.list_pred_analysis_mono_overview.count() == 0: 6141 # 6142 # self._view.ui.btn_pred_analysis_mono_back_pred_setup.show() 6143 # self._view.ui.btn_pred_analysis_mono_remove.hide() 6144 6145 def check_mono_pred_analysis_if_same_no_of_chains_selected(self) -> None: 6146 """Checks if the same number of chains were selected.""" 6147 self._view.ui.btn_pred_analysis_mono_next_4.setEnabled(False) 6148 if self.no_of_selected_chains == len(self._view.ui.list_pred_analysis_mono_model_chains.selectedItems()): 6149 self._view.ui.btn_pred_analysis_mono_next_4.setEnabled(True) 6150 6151 prot_1_name = self._view.ui.lbl_pred_analysis_mono_prot_struct_1.text() 6152 prot_1_chains = [] 6153 for chain in self._view.ui.list_pred_analysis_mono_ref_chains.selectedItems(): 6154 prot_1_chains.append(chain.text()) 6155 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 6156 prot_2_name = self._view.ui.lbl_pred_analysis_mono_prot_struct_2.text() 6157 prot_2_chains = [] 6158 for chain in self._view.ui.list_pred_analysis_mono_model_chains.selectedItems(): 6159 prot_2_chains.append(chain.text()) 6160 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 6161 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 6162 for tmp_row in range(self._view.ui.list_pred_analysis_mono_overview.count()): 6163 if analysis_name == self._view.ui.list_pred_analysis_mono_overview.item(tmp_row).text(): 6164 self._view.ui.btn_pred_analysis_mono_next_4.setEnabled(False) 6165 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_mono_next_4) 6166 return 6167 6168 def check_mono_pred_analysis_if_prot_structs_are_filled(self) -> None: 6169 """Checks if two proteins were selected.""" 6170 prot_1 = self._view.ui.box_pred_analysis_mono_prot_struct_1.itemText( 6171 self._view.ui.box_pred_analysis_mono_prot_struct_1.currentIndex(), 6172 ) 6173 prot_2 = self._view.ui.box_pred_analysis_mono_prot_struct_2.itemText( 6174 self._view.ui.box_pred_analysis_mono_prot_struct_2.currentIndex(), 6175 ) 6176 if prot_1 != "" and prot_2 != "": 6177 self._view.ui.btn_pred_analysis_mono_next_2.setEnabled(True) 6178 else: 6179 self._view.ui.btn_pred_analysis_mono_next_2.setEnabled(False) 6180 6181 def count_mono_pred_analysis_selected_chains_for_prot_struct_1(self) -> None: 6182 """Counts the number of chains selected in protein 1.""" 6183 self.no_of_selected_chains = len(self._view.ui.list_pred_analysis_mono_ref_chains.selectedItems()) 6184 if self.no_of_selected_chains > 0: 6185 self._view.ui.btn_pred_analysis_mono_next_3.setEnabled(True) 6186 else: 6187 self._view.ui.btn_pred_analysis_mono_next_3.setEnabled(False) 6188 6189 # </editor-fold> 6190 6191 # </editor-fold> 6192 6193 def switch_monomer_pred_analysis_tab(self) -> None: 6194 """Switches the tabs from prediction to analysis and vice versa.""" 6195 if self._view.ui.tabWidget.currentIndex() == 0: 6196 # goes from prediction to analysis 6197 self._view.ui.tabWidget.setTabEnabled(1, True) 6198 self._view.ui.tabWidget.setTabEnabled(0, False) 6199 self._view.ui.tabWidget.setCurrentIndex(1) 6200 gui_elements_to_show = [ 6201 self._view.ui.lbl_pred_analysis_mono_overview, 6202 self._view.ui.list_pred_analysis_mono_overview, 6203 self._view.ui.btn_pred_analysis_mono_add, 6204 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 6205 ] 6206 gui_elements_to_hide = [ 6207 self._view.ui.btn_pred_analysis_mono_remove, 6208 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 6209 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 6210 self._view.ui.lbl_analysis_batch_vs_2, 6211 self._view.ui.lbl_pred_analysis_mono_ref_chains, 6212 self._view.ui.list_pred_analysis_mono_ref_chains, 6213 self._view.ui.btn_pred_analysis_mono_back_4, 6214 self._view.ui.btn_pred_analysis_mono_next_3, 6215 self._view.ui.box_pred_analysis_mono_prot_struct_1, 6216 self._view.ui.box_pred_analysis_mono_prot_struct_2, 6217 self._view.ui.btn_pred_analysis_mono_back_3, 6218 self._view.ui.btn_pred_analysis_mono_next_2, 6219 self._view.ui.lbl_pred_analysis_mono_model_chains, 6220 self._view.ui.list_pred_analysis_mono_model_chains, 6221 self._view.ui.btn_pred_analysis_mono_back_5, 6222 self._view.ui.btn_pred_analysis_mono_next_4, 6223 self._view.ui.lbl_pred_analysis_mono_images, 6224 self._view.ui.cb_pred_analysis_mono_images, 6225 self._view.ui.btn_pred_analysis_mono_start, 6226 ] 6227 gui_utils.show_gui_elements(gui_elements_to_show) 6228 gui_utils.hide_gui_elements(gui_elements_to_hide) 6229 if self._view.ui.list_pred_analysis_mono_overview.count() > 0: 6230 self._view.ui.btn_pred_analysis_mono_remove.show() 6231 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(False) 6232 self._view.ui.btn_pred_analysis_mono_start.show() 6233 self._view.ui.lbl_pred_analysis_mono_images.show() 6234 self._view.ui.cb_pred_analysis_mono_images.show() 6235 else: 6236 # goes from analysis to prediction 6237 if self._view.ui.list_pred_analysis_mono_overview.count() > 0: 6238 gui_elements_to_show = [ 6239 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 6240 self._view.ui.table_pred_analysis_mono_prot_to_predict, 6241 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 6242 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 6243 ] 6244 gui_elements_to_hide = [ 6245 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 6246 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 6247 self._view.ui.lbl_pred_analysis_mono_prot_name, 6248 self._view.ui.txt_pred_analysis_mono_prot_name, 6249 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 6250 self._view.ui.btn_pred_analysis_mono_back, 6251 self._view.ui.btn_pred_analysis_mono_next, 6252 self._view.ui.lbl_pred_analysis_mono_seq_name, 6253 self._view.ui.txt_pred_analysis_mono_seq_name, 6254 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 6255 self._view.ui.btn_pred_analysis_mono_back_2, 6256 self._view.ui.btn_pred_analysis_mono_add_protein, 6257 self._view.ui.lbl_pred_mono_advanced_config_2, 6258 self._view.ui.btn_pred_mono_advanced_config_2, 6259 ] 6260 gui_utils.show_gui_elements(gui_elements_to_show) 6261 gui_utils.hide_gui_elements(gui_elements_to_hide) 6262 else: 6263 gui_elements_to_show = [ 6264 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 6265 self._view.ui.table_pred_analysis_mono_prot_to_predict, 6266 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 6267 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 6268 self._view.ui.lbl_pred_mono_advanced_config_2, 6269 self._view.ui.btn_pred_mono_advanced_config_2, 6270 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 6271 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 6272 ] 6273 gui_elements_to_hide = [ 6274 self._view.ui.lbl_pred_analysis_mono_prot_name, 6275 self._view.ui.txt_pred_analysis_mono_prot_name, 6276 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 6277 self._view.ui.btn_pred_analysis_mono_back, 6278 self._view.ui.btn_pred_analysis_mono_next, 6279 self._view.ui.lbl_pred_analysis_mono_seq_name, 6280 self._view.ui.txt_pred_analysis_mono_seq_name, 6281 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 6282 self._view.ui.btn_pred_analysis_mono_back_2, 6283 self._view.ui.btn_pred_analysis_mono_add_protein, 6284 ] 6285 gui_utils.show_gui_elements(gui_elements_to_show) 6286 gui_utils.hide_gui_elements(gui_elements_to_hide) 6287 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.setEnabled(False) 6288 self._view.ui.tabWidget.setTabEnabled(0, True) 6289 self._view.ui.tabWidget.setTabEnabled(1, False) 6290 self._view.ui.tabWidget.setCurrentIndex(0) 6291 6292 # </editor-fold> 6293 6294 # <editor-fold desc="Multimer prediction + analysis"> 6295 def _init_multi_pred_analysis_page(self) -> None: 6296 """Clears the text boxes and sets the default values for the gui elements.""" 6297 # <editor-fold desc="Prediction section"> 6298 # clears everything 6299 self._view.ui.txt_pred_analysis_multi_prot_name.clear() 6300 self._view.ui.txt_pred_analysis_multi_prot_seq.clear() 6301 self._view.ui.list_pred_analysis_multi_prot_seq_overview.clear() 6302 for i in range(self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() - 1, -1, -1): 6303 self._view.ui.table_pred_analysis_multi_prot_to_predict.removeRow(i) 6304 6305 # sets up defaults: Prediction 6306 self._view.ui.btn_pred_analysis_multi_next.setEnabled(False) 6307 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2.setEnabled(False) 6308 self._view.ui.lbl_pred_analysis_multi_prot_name_status.setText("") 6309 self._view.ui.lbl_pred_analysis_multi_prot_seq_status.setText("") 6310 6311 # </editor-fold> 6312 6313 # <editor-fold desc="Analysis section"> 6314 self._view.ui.list_pred_analysis_multi_overview.clear() 6315 self._view.ui.btn_pred_analysis_multi_remove.hide() 6316 6317 # </editor-fold> 6318 6319 # self.multi_pred_analysis_show_protein_overview() 6320 6321 def display_multimer_pred_analysis(self) -> None: 6322 """Displays the multimer prediction + analysis page.""" 6323 # checks internet connection 6324 if not tools.check_internet_connectivity(): 6325 gui_utils.no_internet_dialog() 6326 return 6327 6328 self._init_multi_pred_analysis_page() 6329 self._view.ui.table_pred_analysis_multi_prot_to_predict.clear() 6330 self._view.ui.table_pred_analysis_multi_prot_to_predict.setHorizontalHeaderItem( 6331 0, 6332 QtWidgets.QTableWidgetItem("Chain"), 6333 ) 6334 self._view.ui.table_pred_analysis_multi_prot_to_predict.setHorizontalHeaderItem( 6335 1, 6336 QtWidgets.QTableWidgetItem("Sequence"), 6337 ) 6338 self._view.ui.table_pred_analysis_multi_prot_to_predict.resizeColumnsToContents() 6339 gui_elements_to_show = [ 6340 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6341 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6342 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6343 ] 6344 gui_elements_to_hide = [ 6345 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6346 self._view.ui.lbl_pred_analysis_multi_prot_name, 6347 self._view.ui.txt_pred_analysis_multi_prot_name, 6348 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6349 self._view.ui.btn_pred_analysis_multi_back, 6350 self._view.ui.btn_pred_analysis_multi_next, 6351 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6352 self._view.ui.txt_pred_analysis_multi_prot_seq, 6353 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6354 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6355 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6356 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6357 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6358 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6359 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6360 self._view.ui.btn_pred_analysis_multi_back_2, 6361 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6362 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6363 self._view.ui.btn_pred_analysis_multi_advanced_config, 6364 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6365 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6366 ] 6367 gui_utils.show_gui_elements(gui_elements_to_show) 6368 gui_utils.hide_gui_elements(gui_elements_to_hide) 6369 if self._view.ui.tabWidget_2.currentIndex() == 1: 6370 self._view.ui.tabWidget_2.setCurrentIndex(0) 6371 self._view.ui.tabWidget_2.setTabEnabled(1, False) 6372 self._view.ui.tabWidget_2.setTabEnabled(0, True) 6373 tools.switch_page( 6374 self._view.ui.stackedWidget, 6375 self._view.ui.lbl_page_title, 6376 22, 6377 "Multimer Prediction + Analysis", 6378 ) 6379 self.last_sidebar_button = styles.color_sidebar_buttons( 6380 self.last_sidebar_button, 6381 self._view.ui.btn_pred_analysis_multimer_page, 6382 ) 6383 self._view.ui.table_pred_analysis_multi_prot_to_predict.setEnabled(True) 6384 6385 # <editor-fold desc="Prediction section"> 6386 def multi_pred_analysis_validate_protein_name(self) -> None: 6387 """Validates the input of the protein name in real-time.""" 6388 if safeguard.Safeguard.check_if_value_is_in_table_v_header( 6389 self._view.ui.txt_pred_analysis_multi_prot_name.text(), 6390 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6391 ): 6392 self._view.ui.lbl_pred_analysis_multi_prot_name_status.setText("Protein name already used.") 6393 self._view.ui.btn_pred_analysis_multi_next.setEnabled(False) 6394 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_multi_next) 6395 else: 6396 self._view.ui.btn_pred_analysis_multi_next.setEnabled(True) 6397 tools.validate_protein_name( 6398 self._view.ui.txt_pred_analysis_multi_prot_name, 6399 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6400 self._view.ui.btn_pred_analysis_multi_next, 6401 ) 6402 6403 def multi_pred_analysis_validate_protein_sequence(self) -> None: 6404 """Validates the input of the protein sequence in real-time.""" 6405 tools.validate_protein_sequence( 6406 self._view.ui.txt_pred_analysis_multi_prot_seq, 6407 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6408 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6409 ) 6410 6411 def multi_pred_analysis_check_if_list_is_empty(self) -> None: 6412 """Checks if the list of sequences of the protein is empty.""" 6413 if self._view.ui.list_pred_analysis_multi_prot_seq_overview.count() == 0: 6414 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2.setEnabled(False) 6415 else: 6416 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2.setEnabled(True) 6417 6418 def multi_pred_analysis_add_sequence_to_list(self) -> None: 6419 """Adds the entered sequence to the sequences of the protein.""" 6420 self._view.ui.list_pred_analysis_multi_prot_seq_overview.addItem( 6421 QtWidgets.QListWidgetItem(self._view.ui.txt_pred_analysis_multi_prot_seq.toPlainText()), 6422 ) 6423 self.multi_pred_analysis_check_if_list_is_empty() 6424 6425 def multi_pred_analysis_remove_sequence_to_list(self) -> None: 6426 """Removes the entered sequence from the sequences of the protein.""" 6427 self._view.ui.list_pred_analysis_multi_prot_seq_overview.takeItem( 6428 self._view.ui.list_pred_analysis_multi_prot_seq_overview.currentRow(), 6429 ) 6430 self.multi_pred_analysis_check_if_list_is_empty() 6431 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove.setEnabled(False) 6432 6433 def multi_pred_analysis_check_if_table_is_empty(self) -> None: 6434 """Checks if the list of proteins to predict is empty.""" 6435 if self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() == 0: 6436 styles.color_button_not_ready(self._view.ui.btn_pred_multi_predict) 6437 gui_elements_to_show = [ 6438 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6439 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6440 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6441 ] 6442 gui_elements_to_hide = [ 6443 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6444 self._view.ui.lbl_pred_analysis_multi_prot_name, 6445 self._view.ui.txt_pred_analysis_multi_prot_name, 6446 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6447 self._view.ui.btn_pred_analysis_multi_back, 6448 self._view.ui.btn_pred_analysis_multi_next, 6449 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6450 self._view.ui.txt_pred_analysis_multi_prot_seq, 6451 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6452 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6453 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6454 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6455 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6456 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6457 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6458 self._view.ui.btn_pred_analysis_multi_back_2, 6459 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6460 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6461 self._view.ui.btn_pred_analysis_multi_advanced_config, 6462 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6463 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6464 ] 6465 gui_utils.show_gui_elements(gui_elements_to_show) 6466 gui_utils.hide_gui_elements(gui_elements_to_hide) 6467 self._view.ui.btn_pred_multi_predict.setEnabled(False) 6468 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False) 6469 else: 6470 self._view.ui.btn_pred_multi_predict.setEnabled(True) 6471 gui_elements_to_show = [ 6472 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6473 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6474 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6475 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6476 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6477 self._view.ui.btn_pred_analysis_multi_advanced_config, 6478 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6479 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6480 ] 6481 gui_elements_to_hide = [ 6482 self._view.ui.lbl_pred_analysis_multi_prot_name, 6483 self._view.ui.txt_pred_analysis_multi_prot_name, 6484 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6485 self._view.ui.btn_pred_analysis_multi_back, 6486 self._view.ui.btn_pred_analysis_multi_next, 6487 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6488 self._view.ui.txt_pred_analysis_multi_prot_seq, 6489 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6490 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6491 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6492 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6493 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6494 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6495 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6496 self._view.ui.btn_pred_analysis_multi_back_2, 6497 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6498 ] 6499 gui_utils.show_gui_elements(gui_elements_to_show) 6500 gui_utils.hide_gui_elements(gui_elements_to_hide) 6501 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False) 6502 6503 def multi_pred_analysis_add_protein_to_predict(self) -> None: 6504 """Adds the proteins to the list of proteins to predict.""" 6505 for i in range(self._view.ui.list_pred_analysis_multi_prot_seq_overview.count()): 6506 self._view.ui.table_pred_analysis_multi_prot_to_predict.setRowCount( 6507 self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() + 1, 6508 ) 6509 self._view.ui.table_pred_analysis_multi_prot_to_predict.insertRow( 6510 self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() + 1, 6511 ) 6512 tmp_chain_seq = ( 6513 constants.chain_dict.get(i), 6514 self._view.ui.list_pred_analysis_multi_prot_seq_overview.item(i).text(), 6515 ) 6516 self._view.ui.table_pred_analysis_multi_prot_to_predict.setItem( 6517 self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() - 1, 6518 0, 6519 QtWidgets.QTableWidgetItem(tmp_chain_seq[0]), 6520 ) 6521 self._view.ui.table_pred_analysis_multi_prot_to_predict.setItem( 6522 self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() - 1, 6523 1, 6524 QtWidgets.QTableWidgetItem(tmp_chain_seq[1]), 6525 ) 6526 name_item = QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_analysis_multi_prot_name.text()) 6527 self._view.ui.table_pred_analysis_multi_prot_to_predict.setVerticalHeaderItem( 6528 self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() - 1, 6529 name_item, 6530 ) 6531 self._view.ui.table_pred_analysis_multi_prot_to_predict.resizeColumnsToContents() 6532 self.multi_pred_analysis_check_if_table_is_empty() 6533 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove.setEnabled(False) 6534 6535 def multi_pred_analysis_remove_protein_to_predict(self) -> None: 6536 """Removes the selected protein from the list of proteins to predict.""" 6537 if self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() == 1: 6538 self._view.ui.table_pred_analysis_multi_prot_to_predict.removeRow(0) 6539 else: 6540 self._view.ui.table_pred_analysis_multi_prot_to_predict.removeRow( 6541 self._view.ui.table_pred_analysis_multi_prot_to_predict.currentRow(), 6542 ) 6543 prot_name = self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem( 6544 self._view.ui.table_pred_analysis_multi_prot_to_predict.currentRow(), 6545 ).text() 6546 for i in range(self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount()): 6547 if self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem(i).text() == prot_name: 6548 self._view.ui.table_pred_analysis_multi_prot_to_predict.setItem( 6549 i, 6550 0, 6551 QtWidgets.QTableWidgetItem(constants.chain_dict.get(i)), 6552 ) 6553 self.multi_pred_analysis_check_if_table_is_empty() 6554 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove.setEnabled(False) 6555 6556 def multi_pred_analysis_add(self) -> None: 6557 """Shows the gui elements for the protein name.""" 6558 gui_elements_to_show = [ 6559 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6560 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6561 self._view.ui.lbl_pred_analysis_multi_prot_name, 6562 self._view.ui.txt_pred_analysis_multi_prot_name, 6563 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6564 self._view.ui.btn_pred_analysis_multi_back, 6565 self._view.ui.btn_pred_analysis_multi_next, 6566 ] 6567 gui_elements_to_hide = [ 6568 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6569 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6570 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6571 self._view.ui.txt_pred_analysis_multi_prot_seq, 6572 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6573 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6574 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6575 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6576 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6577 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6578 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6579 self._view.ui.btn_pred_analysis_multi_back_2, 6580 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6581 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6582 self._view.ui.btn_pred_analysis_multi_advanced_config, 6583 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6584 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6585 ] 6586 gui_utils.show_gui_elements(gui_elements_to_show) 6587 gui_utils.hide_gui_elements(gui_elements_to_hide) 6588 gui_utils.enable_text_box( 6589 self._view.ui.txt_pred_analysis_multi_prot_name, 6590 self._view.ui.lbl_pred_analysis_multi_prot_name, 6591 ) 6592 gui_utils.disable_text_box( 6593 self._view.ui.txt_pred_analysis_multi_prot_seq, 6594 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6595 ) 6596 self._view.ui.btn_pred_analysis_multi_next.setEnabled(False) 6597 self._view.ui.txt_pred_analysis_multi_prot_name.clear() 6598 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_multi_next) 6599 if self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() > 0: 6600 try: 6601 self._view.ui.table_pred_analysis_multi_prot_to_predict.currentItem().setSelected(False) 6602 except AttributeError: 6603 constants.PYSSA_LOGGER.debug("No selection on Local Multimer Prediction in overview table.") 6604 6605 def multi_pred_analysis_back(self) -> None: 6606 """Hides the gui elements for the protein name.""" 6607 gui_elements_to_show = [ 6608 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6609 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6610 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6611 ] 6612 gui_elements_to_hide = [ 6613 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6614 self._view.ui.lbl_pred_analysis_multi_prot_name, 6615 self._view.ui.txt_pred_analysis_multi_prot_name, 6616 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6617 self._view.ui.btn_pred_analysis_multi_back, 6618 self._view.ui.btn_pred_analysis_multi_next, 6619 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6620 self._view.ui.txt_pred_analysis_multi_prot_seq, 6621 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6622 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6623 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6624 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6625 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6626 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6627 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6628 self._view.ui.btn_pred_analysis_multi_back_2, 6629 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6630 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6631 self._view.ui.btn_pred_analysis_multi_advanced_config, 6632 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6633 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6634 ] 6635 gui_utils.show_gui_elements(gui_elements_to_show) 6636 gui_utils.hide_gui_elements(gui_elements_to_hide) 6637 self.multi_pred_analysis_check_if_table_is_empty() 6638 6639 def multi_pred_analysis_next(self) -> None: 6640 """Shows the gui elements for the protein sequence.""" 6641 gui_elements_to_show = [ 6642 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6643 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6644 self._view.ui.lbl_pred_analysis_multi_prot_name, 6645 self._view.ui.txt_pred_analysis_multi_prot_name, 6646 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6647 self._view.ui.txt_pred_analysis_multi_prot_seq, 6648 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6649 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6650 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6651 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6652 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6653 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6654 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6655 self._view.ui.btn_pred_analysis_multi_back_2, 6656 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6657 ] 6658 gui_elements_to_hide = [ 6659 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6660 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6661 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6662 self._view.ui.btn_pred_analysis_multi_back, 6663 self._view.ui.btn_pred_analysis_multi_next, 6664 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6665 self._view.ui.btn_pred_analysis_multi_advanced_config, 6666 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6667 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6668 ] 6669 gui_utils.show_gui_elements(gui_elements_to_show) 6670 gui_utils.hide_gui_elements(gui_elements_to_hide) 6671 gui_utils.enable_text_box( 6672 self._view.ui.txt_pred_analysis_multi_prot_seq, 6673 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6674 ) 6675 gui_utils.disable_text_box( 6676 self._view.ui.txt_pred_analysis_multi_prot_name, 6677 self._view.ui.lbl_pred_analysis_multi_prot_name, 6678 ) 6679 self._view.ui.txt_pred_analysis_multi_prot_seq.clear() 6680 self._view.ui.list_pred_analysis_multi_prot_seq_overview.clear() 6681 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2.setEnabled(False) 6682 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove.setEnabled(False) 6683 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2) 6684 6685 def multi_pred_analysis_back_2(self) -> None: 6686 """Hides the gui elements for the protein sequence.""" 6687 gui_elements_to_show = [ 6688 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6689 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6690 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6691 self._view.ui.btn_pred_analysis_multi_back, 6692 self._view.ui.btn_pred_analysis_multi_next, 6693 self._view.ui.lbl_pred_analysis_multi_prot_name, 6694 self._view.ui.txt_pred_analysis_multi_prot_name, 6695 ] 6696 gui_elements_to_hide = [ 6697 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6698 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6699 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6700 self._view.ui.txt_pred_analysis_multi_prot_seq, 6701 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6702 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6703 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6704 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6705 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6706 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6707 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6708 self._view.ui.btn_pred_analysis_multi_back_2, 6709 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6710 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6711 self._view.ui.btn_pred_analysis_multi_advanced_config, 6712 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6713 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6714 ] 6715 gui_utils.show_gui_elements(gui_elements_to_show) 6716 gui_utils.hide_gui_elements(gui_elements_to_hide) 6717 gui_utils.enable_text_box( 6718 self._view.ui.txt_pred_analysis_multi_prot_name, 6719 self._view.ui.lbl_pred_analysis_multi_prot_name, 6720 ) 6721 gui_utils.disable_text_box( 6722 self._view.ui.txt_pred_analysis_multi_prot_seq, 6723 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6724 ) 6725 6726 def multi_pred_analysis_prot_seq_overview_item_changed(self) -> None: 6727 """Enables the remove button of the list of sequences of the protein.""" 6728 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove.setEnabled(True) 6729 6730 def multi_pred_analysis_prot_to_predict_item_changed(self) -> None: 6731 """Enables the remove button of the list of proteins to predict.""" 6732 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove.setEnabled(True) 6733 6734 # </editor-fold> 6735 6736 def switch_multimer_pred_analysis_tab(self) -> None: 6737 """Switches the tabs from prediction to analysis and vice versa.""" 6738 if self._view.ui.tabWidget_2.currentIndex() == 0: 6739 # goes from prediction to analysis 6740 self._view.ui.tabWidget_2.setCurrentIndex(1) 6741 gui_elements_to_show = [ 6742 self._view.ui.lbl_pred_analysis_multi_overview, 6743 self._view.ui.list_pred_analysis_multi_overview, 6744 self._view.ui.btn_pred_analysis_multi_add, 6745 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 6746 ] 6747 gui_elements_to_hide = [ 6748 self._view.ui.btn_pred_analysis_multi_remove, 6749 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 6750 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 6751 self._view.ui.lbl_analysis_batch_vs_3, 6752 self._view.ui.lbl_pred_analysis_multi_ref_chains, 6753 self._view.ui.list_pred_analysis_multi_ref_chains, 6754 self._view.ui.btn_pred_analysis_multi_back_4, 6755 self._view.ui.btn_pred_analysis_multi_next_3, 6756 self._view.ui.box_pred_analysis_multi_prot_struct_1, 6757 self._view.ui.box_pred_analysis_multi_prot_struct_2, 6758 self._view.ui.btn_pred_analysis_multi_back_3, 6759 self._view.ui.btn_pred_analysis_multi_next_2, 6760 self._view.ui.lbl_pred_analysis_multi_model_chains, 6761 self._view.ui.list_pred_analysis_multi_model_chains, 6762 self._view.ui.btn_pred_analysis_multi_back_5, 6763 self._view.ui.btn_pred_analysis_multi_next_4, 6764 self._view.ui.lbl_pred_analysis_multi_images, 6765 self._view.ui.cb_pred_analysis_multi_images, 6766 self._view.ui.btn_pred_analysis_multi_start, 6767 ] 6768 gui_utils.show_gui_elements(gui_elements_to_show) 6769 gui_utils.hide_gui_elements(gui_elements_to_hide) 6770 self._view.ui.tabWidget_2.setTabEnabled(1, True) 6771 self._view.ui.tabWidget_2.setTabEnabled(0, False) 6772 if self._view.ui.list_pred_analysis_multi_overview.count() > 0: 6773 self._view.ui.btn_pred_analysis_multi_remove.show() 6774 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(False) 6775 self._view.ui.btn_pred_analysis_multi_start.show() 6776 self._view.ui.lbl_pred_analysis_multi_images.show() 6777 self._view.ui.cb_pred_analysis_multi_images.show() 6778 else: 6779 # goes from analysis to prediction 6780 self._view.ui.tabWidget_2.setCurrentIndex(0) 6781 if self._view.ui.list_pred_analysis_multi_overview.count() > 0: 6782 gui_elements_to_show = [ 6783 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6784 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6785 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6786 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6787 ] 6788 gui_elements_to_hide = [ 6789 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6790 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6791 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6792 self._view.ui.btn_pred_analysis_multi_advanced_config, 6793 self._view.ui.lbl_pred_analysis_multi_prot_name, 6794 self._view.ui.txt_pred_analysis_multi_prot_name, 6795 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6796 self._view.ui.btn_pred_analysis_multi_back, 6797 self._view.ui.btn_pred_analysis_multi_next, 6798 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6799 self._view.ui.txt_pred_analysis_multi_prot_seq, 6800 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6801 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6802 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6803 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6804 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6805 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6806 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6807 self._view.ui.btn_pred_analysis_multi_back_2, 6808 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6809 ] 6810 gui_utils.show_gui_elements(gui_elements_to_show) 6811 gui_utils.hide_gui_elements(gui_elements_to_hide) 6812 else: 6813 gui_elements_to_show = [ 6814 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6815 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6816 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6817 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6818 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6819 self._view.ui.btn_pred_analysis_multi_advanced_config, 6820 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6821 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6822 ] 6823 gui_elements_to_hide = [ 6824 self._view.ui.lbl_pred_analysis_multi_prot_name, 6825 self._view.ui.txt_pred_analysis_multi_prot_name, 6826 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6827 self._view.ui.btn_pred_analysis_multi_back, 6828 self._view.ui.btn_pred_analysis_multi_next, 6829 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6830 self._view.ui.txt_pred_analysis_multi_prot_seq, 6831 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6832 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6833 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6834 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6835 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6836 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6837 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6838 self._view.ui.btn_pred_analysis_multi_back_2, 6839 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6840 ] 6841 gui_utils.show_gui_elements(gui_elements_to_show) 6842 gui_utils.hide_gui_elements(gui_elements_to_hide) 6843 self._view.ui.tabWidget_2.setTabEnabled(0, True) 6844 self._view.ui.tabWidget_2.setTabEnabled(1, False) 6845 6846 # <editor-fold desc="Analysis section"> 6847 def multi_pred_analysis_structure_analysis_add(self) -> None: 6848 """Shows the gui elements to choose the two proteins.""" 6849 gui_elements_to_show = [ 6850 self._view.ui.lbl_pred_analysis_multi_overview, 6851 self._view.ui.list_pred_analysis_multi_overview, 6852 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 6853 self._view.ui.box_pred_analysis_multi_prot_struct_1, 6854 self._view.ui.lbl_analysis_batch_vs_3, 6855 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 6856 self._view.ui.box_pred_analysis_multi_prot_struct_2, 6857 self._view.ui.btn_pred_analysis_multi_back_3, 6858 self._view.ui.btn_pred_analysis_multi_next_2, 6859 ] 6860 gui_elements_to_hide = [ 6861 self._view.ui.btn_pred_analysis_multi_remove, 6862 self._view.ui.btn_pred_analysis_multi_add, 6863 self._view.ui.lbl_pred_analysis_multi_ref_chains, 6864 self._view.ui.list_pred_analysis_multi_ref_chains, 6865 self._view.ui.btn_pred_analysis_multi_back_4, 6866 self._view.ui.btn_pred_analysis_multi_next_3, 6867 self._view.ui.lbl_pred_analysis_multi_model_chains, 6868 self._view.ui.list_pred_analysis_multi_model_chains, 6869 self._view.ui.btn_pred_analysis_multi_back_5, 6870 self._view.ui.btn_pred_analysis_multi_next_4, 6871 self._view.ui.lbl_pred_analysis_multi_images, 6872 self._view.ui.cb_pred_analysis_multi_images, 6873 self._view.ui.btn_pred_analysis_multi_start, 6874 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 6875 ] 6876 gui_utils.show_gui_elements(gui_elements_to_show) 6877 gui_utils.hide_gui_elements(gui_elements_to_hide) 6878 self._view.ui.lbl_pred_analysis_multi_prot_struct_1.clear() 6879 self._view.ui.lbl_pred_analysis_multi_prot_struct_2.clear() 6880 self._view.ui.lbl_pred_analysis_multi_prot_struct_1.setText("Protein structure 1") 6881 self._view.ui.lbl_pred_analysis_multi_prot_struct_2.setText("Protein structure 2") 6882 self.fill_multi_pred_analysis_protein_boxes() 6883 if self._view.ui.list_pred_analysis_multi_overview.count() > 0: 6884 try: 6885 self._view.ui.list_pred_analysis_multi_overview.currentItem().setSelected(False) 6886 except AttributeError: 6887 constants.PYSSA_LOGGER.debug("No selection in struction analysis overview.") 6888 6889 def multi_pred_analysis_structure_analysis_back_3(self) -> None: 6890 """Hides the gui elements to choose the two proteins.""" 6891 gui_elements_to_show = [ 6892 self._view.ui.lbl_pred_analysis_multi_overview, 6893 self._view.ui.list_pred_analysis_multi_overview, 6894 self._view.ui.btn_pred_analysis_multi_add, 6895 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 6896 ] 6897 gui_elements_to_hide = [ 6898 self._view.ui.btn_pred_analysis_multi_remove, 6899 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 6900 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 6901 self._view.ui.lbl_analysis_batch_vs_3, 6902 self._view.ui.lbl_pred_analysis_multi_ref_chains, 6903 self._view.ui.list_pred_analysis_multi_ref_chains, 6904 self._view.ui.btn_pred_analysis_multi_back_4, 6905 self._view.ui.btn_pred_analysis_multi_next_3, 6906 self._view.ui.box_pred_analysis_multi_prot_struct_1, 6907 self._view.ui.box_pred_analysis_multi_prot_struct_2, 6908 self._view.ui.btn_pred_analysis_multi_back_3, 6909 self._view.ui.btn_pred_analysis_multi_next_2, 6910 self._view.ui.lbl_pred_analysis_multi_model_chains, 6911 self._view.ui.list_pred_analysis_multi_model_chains, 6912 self._view.ui.btn_pred_analysis_multi_back_5, 6913 self._view.ui.btn_pred_analysis_multi_next_4, 6914 self._view.ui.lbl_pred_analysis_multi_images, 6915 self._view.ui.cb_pred_analysis_multi_images, 6916 self._view.ui.btn_pred_analysis_multi_start, 6917 ] 6918 gui_utils.show_gui_elements(gui_elements_to_show) 6919 gui_utils.hide_gui_elements(gui_elements_to_hide) 6920 if self._view.ui.list_pred_analysis_multi_overview.count() > 0: 6921 self._view.ui.btn_pred_analysis_multi_remove.show() 6922 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(False) 6923 self._view.ui.btn_pred_analysis_multi_start.show() 6924 self._view.ui.lbl_pred_analysis_multi_images.show() 6925 self._view.ui.cb_pred_analysis_multi_images.show() 6926 6927 def multi_pred_analysis_structure_analysis_next_3(self) -> None: 6928 """Shows the gui elements to select the chains in protein 2.""" 6929 gui_elements_to_show = [ 6930 self._view.ui.lbl_pred_analysis_multi_overview, 6931 self._view.ui.list_pred_analysis_multi_overview, 6932 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 6933 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 6934 self._view.ui.lbl_analysis_batch_vs_3, 6935 self._view.ui.lbl_pred_analysis_multi_ref_chains, 6936 self._view.ui.list_pred_analysis_multi_ref_chains, 6937 self._view.ui.lbl_pred_analysis_multi_model_chains, 6938 self._view.ui.list_pred_analysis_multi_model_chains, 6939 self._view.ui.btn_pred_analysis_multi_back_5, 6940 self._view.ui.btn_pred_analysis_multi_next_4, 6941 ] 6942 gui_elements_to_hide = [ 6943 self._view.ui.btn_pred_analysis_multi_remove, 6944 self._view.ui.btn_pred_analysis_multi_add, 6945 self._view.ui.box_pred_analysis_multi_prot_struct_1, 6946 self._view.ui.box_pred_analysis_multi_prot_struct_2, 6947 self._view.ui.btn_pred_analysis_multi_back_3, 6948 self._view.ui.btn_pred_analysis_multi_next_2, 6949 self._view.ui.btn_pred_analysis_multi_back_4, 6950 self._view.ui.btn_pred_analysis_multi_next_3, 6951 self._view.ui.lbl_pred_analysis_multi_images, 6952 self._view.ui.cb_pred_analysis_multi_images, 6953 self._view.ui.btn_pred_analysis_multi_start, 6954 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 6955 ] 6956 gui_utils.show_gui_elements(gui_elements_to_show) 6957 gui_utils.hide_gui_elements(gui_elements_to_hide) 6958 self._view.ui.list_pred_analysis_multi_model_chains.clear() 6959 self._view.ui.list_pred_analysis_multi_ref_chains.setEnabled(False) 6960 self._view.ui.btn_pred_analysis_multi_next_4.setEnabled(False) 6961 6962 for i in range(self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount()): 6963 if ( 6964 self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem(i).text() 6965 == self._view.ui.box_pred_analysis_multi_prot_struct_2.currentText() 6966 ): 6967 self._view.ui.list_pred_analysis_multi_model_chains.addItem( 6968 self._view.ui.table_pred_analysis_multi_prot_to_predict.item(i, 0).text(), 6969 ) 6970 if self._view.ui.list_pred_analysis_multi_model_chains.count() == 0: 6971 tmp_protein = self._current_project.search_protein( 6972 self._view.ui.box_pred_analysis_multi_prot_struct_2.currentText(), 6973 ) 6974 for tmp_chain in tmp_protein.chains: 6975 if tmp_chain.chain_type == "protein_chain": 6976 self._view.ui.list_pred_analysis_multi_model_chains.addItem(tmp_chain.chain_letter) 6977 if len(self._view.ui.list_pred_analysis_multi_ref_chains.selectedItems()) == 1: 6978 self._view.ui.lbl_pred_analysis_multi_model_chains.setText( 6979 f"Select 1 chain in protein structure {self._view.ui.lbl_pred_analysis_multi_prot_struct_2.text()}.", 6980 ) 6981 else: 6982 self._view.ui.lbl_pred_analysis_multi_model_chains.setText( 6983 f"Select {len(self._view.ui.list_pred_analysis_multi_ref_chains.selectedItems())} chains in " 6984 f"protein structure {self._view.ui.lbl_pred_analysis_multi_prot_struct_2.text()}.", 6985 ) 6986 6987 def multi_pred_analysis_structure_analysis_back_4(self) -> None: 6988 """Hides the gui elements to select the chains in protein 1.""" 6989 gui_elements_to_show = [ 6990 self._view.ui.lbl_pred_analysis_multi_overview, 6991 self._view.ui.list_pred_analysis_multi_overview, 6992 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 6993 self._view.ui.box_pred_analysis_multi_prot_struct_1, 6994 self._view.ui.lbl_analysis_batch_vs_3, 6995 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 6996 self._view.ui.box_pred_analysis_multi_prot_struct_2, 6997 self._view.ui.btn_pred_analysis_multi_back_3, 6998 self._view.ui.btn_pred_analysis_multi_next_2, 6999 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 7000 ] 7001 gui_elements_to_hide = [ 7002 self._view.ui.btn_pred_analysis_multi_remove, 7003 self._view.ui.btn_pred_analysis_multi_add, 7004 self._view.ui.lbl_pred_analysis_multi_ref_chains, 7005 self._view.ui.list_pred_analysis_multi_ref_chains, 7006 self._view.ui.btn_pred_analysis_multi_back_4, 7007 self._view.ui.btn_pred_analysis_multi_next_3, 7008 self._view.ui.lbl_pred_analysis_multi_model_chains, 7009 self._view.ui.list_pred_analysis_multi_model_chains, 7010 self._view.ui.btn_pred_analysis_multi_back_5, 7011 self._view.ui.btn_pred_analysis_multi_next_4, 7012 self._view.ui.lbl_pred_analysis_multi_images, 7013 self._view.ui.cb_pred_analysis_multi_images, 7014 self._view.ui.btn_pred_analysis_multi_start, 7015 ] 7016 gui_utils.show_gui_elements(gui_elements_to_show) 7017 gui_utils.hide_gui_elements(gui_elements_to_hide) 7018 self._view.ui.lbl_pred_analysis_multi_prot_struct_1.setText("Protein structure 1") 7019 self._view.ui.lbl_pred_analysis_multi_prot_struct_2.setText("Protein structure 2") 7020 7021 def multi_pred_analysis_structure_analysis_next_4(self) -> None: 7022 """Adds the protein pair to the list of protein pairs to analyze.""" 7023 gui_elements_to_show = [ 7024 self._view.ui.btn_pred_analysis_multi_remove, 7025 self._view.ui.btn_pred_analysis_multi_add, 7026 self._view.ui.lbl_pred_analysis_multi_overview, 7027 self._view.ui.list_pred_analysis_multi_overview, 7028 self._view.ui.lbl_pred_analysis_multi_images, 7029 self._view.ui.cb_pred_analysis_multi_images, 7030 self._view.ui.btn_pred_analysis_multi_start, 7031 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 7032 ] 7033 gui_elements_to_hide = [ 7034 self._view.ui.box_pred_analysis_multi_prot_struct_1, 7035 self._view.ui.box_pred_analysis_multi_prot_struct_2, 7036 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 7037 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 7038 self._view.ui.lbl_analysis_batch_vs_3, 7039 self._view.ui.lbl_pred_analysis_multi_ref_chains, 7040 self._view.ui.list_pred_analysis_multi_ref_chains, 7041 self._view.ui.lbl_pred_analysis_multi_model_chains, 7042 self._view.ui.list_pred_analysis_multi_model_chains, 7043 self._view.ui.btn_pred_analysis_multi_back_3, 7044 self._view.ui.btn_pred_analysis_multi_next_2, 7045 self._view.ui.btn_pred_analysis_multi_back_4, 7046 self._view.ui.btn_pred_analysis_multi_next_3, 7047 self._view.ui.btn_pred_analysis_multi_back_5, 7048 self._view.ui.btn_pred_analysis_multi_next_4, 7049 ] 7050 gui_utils.show_gui_elements(gui_elements_to_show) 7051 gui_utils.hide_gui_elements(gui_elements_to_hide) 7052 prot_1_name = self._view.ui.lbl_pred_analysis_multi_prot_struct_1.text() 7053 prot_1_chains = [] 7054 for chain in self._view.ui.list_pred_analysis_multi_ref_chains.selectedItems(): 7055 prot_1_chains.append(chain.text()) 7056 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 7057 prot_2_name = self._view.ui.lbl_pred_analysis_multi_prot_struct_2.text() 7058 prot_2_chains = [] 7059 for chain in self._view.ui.list_pred_analysis_multi_model_chains.selectedItems(): 7060 prot_2_chains.append(chain.text()) 7061 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 7062 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 7063 item = QtWidgets.QListWidgetItem(analysis_name) 7064 self._view.ui.list_pred_analysis_multi_overview.addItem(item) 7065 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(False) 7066 7067 def multi_pred_analysis_structure_analysis_back_5(self) -> None: 7068 """Hides the gui elements to select the chains in protein 2.""" 7069 gui_elements_to_show = [ 7070 self._view.ui.lbl_pred_analysis_multi_overview, 7071 self._view.ui.list_pred_analysis_multi_overview, 7072 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 7073 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 7074 self._view.ui.lbl_analysis_batch_vs_3, 7075 self._view.ui.lbl_pred_analysis_multi_ref_chains, 7076 self._view.ui.list_pred_analysis_multi_ref_chains, 7077 self._view.ui.btn_pred_analysis_multi_back_4, 7078 self._view.ui.btn_pred_analysis_multi_next_3, 7079 ] 7080 gui_elements_to_hide = [ 7081 self._view.ui.btn_pred_analysis_multi_remove, 7082 self._view.ui.btn_pred_analysis_multi_add, 7083 self._view.ui.box_pred_analysis_multi_prot_struct_1, 7084 self._view.ui.box_pred_analysis_multi_prot_struct_2, 7085 self._view.ui.btn_pred_analysis_multi_back_3, 7086 self._view.ui.btn_pred_analysis_multi_next_2, 7087 self._view.ui.btn_pred_analysis_multi_back_5, 7088 self._view.ui.btn_pred_analysis_multi_next_4, 7089 self._view.ui.lbl_pred_analysis_multi_images, 7090 self._view.ui.cb_pred_analysis_multi_images, 7091 self._view.ui.btn_pred_analysis_multi_start, 7092 self._view.ui.lbl_pred_analysis_multi_model_chains, 7093 self._view.ui.list_pred_analysis_multi_model_chains, 7094 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 7095 ] 7096 gui_utils.show_gui_elements(gui_elements_to_show) 7097 gui_utils.hide_gui_elements(gui_elements_to_hide) 7098 self._view.ui.list_pred_analysis_multi_ref_chains.setEnabled(True) 7099 7100 # tmp_protein = self._current_project.search_protein(self._view.ui.box_pred_analysis_multi_prot_struct_2.currentText()) 7101 # for tmp_chain in tmp_protein.chains: 7102 # if tmp_chain.chain_type == "protein_chain": 7103 # self._view.ui.list_pred_analysis_multi_ref_chains.addItem(tmp_chain.chain_letter) 7104 7105 def multi_pred_analysis_structure_analysis_overview_clicked(self) -> None: 7106 """Enables the remove button.""" 7107 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(True) 7108 7109 def fill_multi_pred_analysis_protein_boxes(self) -> None: 7110 """Fills the combo boxes with the protein names.""" 7111 protein_names = [] 7112 for i in range(self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount()): 7113 protein_names.append(self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem(i).text()) 7114 for tmp_protein in self._current_project.proteins: 7115 protein_names.append(tmp_protein.get_molecule_object()) 7116 protein_names.insert(0, "") 7117 protein_names = list(set(protein_names)) 7118 self._view.ui.box_pred_analysis_multi_prot_struct_1.clear() 7119 self._view.ui.box_pred_analysis_multi_prot_struct_2.clear() 7120 gui_utils.fill_combo_box(self._view.ui.box_pred_analysis_multi_prot_struct_1, protein_names) 7121 gui_utils.fill_combo_box(self._view.ui.box_pred_analysis_multi_prot_struct_2, protein_names) 7122 7123 def remove_multi_pred_analysis_analysis_run(self) -> None: 7124 """Removes the selected protein pair from the list of protein pairs to analyze.""" 7125 self._view.ui.list_pred_analysis_multi_overview.takeItem( 7126 self._view.ui.list_pred_analysis_multi_overview.currentRow(), 7127 ) 7128 gui_elements_to_show = [ 7129 self._view.ui.lbl_pred_analysis_multi_overview, 7130 self._view.ui.list_pred_analysis_multi_overview, 7131 self._view.ui.btn_pred_analysis_multi_add, 7132 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 7133 ] 7134 gui_elements_to_hide = [ 7135 self._view.ui.btn_pred_analysis_multi_remove, 7136 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 7137 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 7138 self._view.ui.lbl_analysis_batch_vs_3, 7139 self._view.ui.lbl_pred_analysis_multi_ref_chains, 7140 self._view.ui.list_pred_analysis_multi_ref_chains, 7141 self._view.ui.btn_pred_analysis_multi_back_4, 7142 self._view.ui.btn_pred_analysis_multi_next_3, 7143 self._view.ui.box_pred_analysis_multi_prot_struct_1, 7144 self._view.ui.box_pred_analysis_multi_prot_struct_2, 7145 self._view.ui.btn_pred_analysis_multi_back_3, 7146 self._view.ui.btn_pred_analysis_multi_next_2, 7147 self._view.ui.lbl_pred_analysis_multi_model_chains, 7148 self._view.ui.list_pred_analysis_multi_model_chains, 7149 self._view.ui.btn_pred_analysis_multi_back_5, 7150 self._view.ui.btn_pred_analysis_multi_next_4, 7151 self._view.ui.lbl_pred_analysis_multi_images, 7152 self._view.ui.cb_pred_analysis_multi_images, 7153 self._view.ui.btn_pred_analysis_multi_start, 7154 ] 7155 gui_utils.show_gui_elements(gui_elements_to_show) 7156 gui_utils.hide_gui_elements(gui_elements_to_hide) 7157 if self._view.ui.list_pred_analysis_multi_overview.count() > 0: 7158 self._view.ui.btn_pred_analysis_multi_remove.show() 7159 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(False) 7160 self._view.ui.btn_pred_analysis_multi_start.show() 7161 self._view.ui.lbl_pred_analysis_multi_images.show() 7162 self._view.ui.cb_pred_analysis_multi_images.show() 7163 # if self._view.ui.list_pred_analysis_multi_overview.count() == 0: 7164 # 7165 # self._view.ui.btn_pred_analysis_multi_back_pred_setup.show() 7166 # self._view.ui.btn_pred_analysis_multi_remove.hide() 7167 7168 def check_multi_pred_analysis_if_same_no_of_chains_selected(self) -> None: 7169 """Checks if the same number of chains were selected.""" 7170 self._view.ui.btn_pred_analysis_multi_next_4.setEnabled(False) 7171 if self.no_of_selected_chains == len(self._view.ui.list_pred_analysis_multi_model_chains.selectedItems()): 7172 self._view.ui.btn_pred_analysis_multi_next_4.setEnabled(True) 7173 7174 prot_1_name = self._view.ui.lbl_pred_analysis_multi_prot_struct_1.text() 7175 prot_1_chains = [] 7176 for chain in self._view.ui.list_pred_analysis_multi_ref_chains.selectedItems(): 7177 prot_1_chains.append(chain.text()) 7178 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 7179 prot_2_name = self._view.ui.lbl_pred_analysis_multi_prot_struct_2.text() 7180 prot_2_chains = [] 7181 for chain in self._view.ui.list_pred_analysis_multi_model_chains.selectedItems(): 7182 prot_2_chains.append(chain.text()) 7183 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 7184 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 7185 for tmp_row in range(self._view.ui.list_pred_analysis_multi_overview.count()): 7186 if analysis_name == self._view.ui.list_pred_analysis_multi_overview.item(tmp_row).text(): 7187 self._view.ui.btn_pred_analysis_multi_next_4.setEnabled(False) 7188 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_multi_next_4) 7189 return 7190 7191 def check_multi_pred_analysis_if_prot_structs_are_filled(self) -> None: 7192 """Checks if two proteins were selected.""" 7193 prot_1 = self._view.ui.box_pred_analysis_multi_prot_struct_1.itemText( 7194 self._view.ui.box_pred_analysis_multi_prot_struct_1.currentIndex(), 7195 ) 7196 prot_2 = self._view.ui.box_pred_analysis_multi_prot_struct_2.itemText( 7197 self._view.ui.box_pred_analysis_multi_prot_struct_2.currentIndex(), 7198 ) 7199 if prot_1 != "" and prot_2 != "": 7200 self._view.ui.btn_pred_analysis_multi_next_2.setEnabled(True) 7201 else: 7202 self._view.ui.btn_pred_analysis_multi_next_2.setEnabled(False) 7203 7204 def count_multi_pred_analysis_selected_chains_for_prot_struct_1(self) -> None: 7205 """Counts the number of chains in protein 1.""" 7206 self.no_of_selected_chains = len(self._view.ui.list_pred_analysis_multi_ref_chains.selectedItems()) 7207 if self.no_of_selected_chains > 0: 7208 self._view.ui.btn_pred_analysis_multi_next_3.setEnabled(True) 7209 else: 7210 self._view.ui.btn_pred_analysis_multi_next_3.setEnabled(False) 7211 7212 # </editor-fold> 7213 # </editor-fold> 7214 7215 # <editor-fold desc="Distance analysis"> 7216 def structure_analysis_add(self) -> None: 7217 """Shows the gui elements to choose the two proteins.""" 7218 gui_elements_to_show = [ 7219 self._view.ui.lbl_analysis_batch_overview, 7220 self._view.ui.list_analysis_batch_overview, 7221 self._view.ui.lbl_analysis_batch_prot_struct_1, 7222 self._view.ui.box_analysis_batch_prot_struct_1, 7223 self._view.ui.lbl_analysis_batch_vs, 7224 self._view.ui.lbl_analysis_batch_prot_struct_2, 7225 self._view.ui.box_analysis_batch_prot_struct_2, 7226 self._view.ui.btn_analysis_batch_back, 7227 self._view.ui.btn_analysis_batch_next, 7228 ] 7229 gui_elements_to_hide = [ 7230 self._view.ui.btn_analysis_batch_remove, 7231 self._view.ui.btn_analysis_batch_add, 7232 self._view.ui.lbl_analysis_batch_ref_chains, 7233 self._view.ui.list_analysis_batch_ref_chains, 7234 self._view.ui.btn_analysis_batch_back_2, 7235 self._view.ui.btn_analysis_batch_next_2, 7236 self._view.ui.lbl_analysis_batch_model_chains, 7237 self._view.ui.list_analysis_batch_model_chains, 7238 self._view.ui.btn_analysis_batch_back_3, 7239 self._view.ui.btn_analysis_batch_next_3, 7240 self._view.ui.lbl_analysis_batch_images, 7241 self._view.ui.cb_analysis_batch_images, 7242 self._view.ui.btn_analysis_batch_start, 7243 ] 7244 7245 gui_utils.show_gui_elements(gui_elements_to_show) 7246 gui_utils.hide_gui_elements(gui_elements_to_hide) 7247 self._view.ui.lbl_analysis_batch_prot_struct_1.clear() 7248 self._view.ui.lbl_analysis_batch_prot_struct_2.clear() 7249 self._view.ui.lbl_analysis_batch_prot_struct_1.setText("Protein structure 1") 7250 self._view.ui.lbl_analysis_batch_prot_struct_2.setText("Protein structure 2") 7251 self.fill_protein_boxes_batch() 7252 if self._view.ui.list_analysis_batch_overview.count() > 0: 7253 try: 7254 self._view.ui.list_analysis_batch_overview.currentItem().setSelected(False) 7255 except AttributeError: 7256 constants.PYSSA_LOGGER.debug("No selection in struction analysis overview.") 7257 7258 def structure_analysis_back(self) -> None: 7259 """Hides the gui elements to choose the two proteins.""" 7260 gui_elements_to_show = [ 7261 self._view.ui.lbl_analysis_batch_overview, 7262 self._view.ui.list_analysis_batch_overview, 7263 self._view.ui.btn_analysis_batch_add, 7264 ] 7265 gui_elements_to_hide = [ 7266 self._view.ui.btn_analysis_batch_remove, 7267 self._view.ui.lbl_analysis_batch_prot_struct_1, 7268 self._view.ui.lbl_analysis_batch_prot_struct_2, 7269 self._view.ui.lbl_analysis_batch_vs, 7270 self._view.ui.lbl_analysis_batch_ref_chains, 7271 self._view.ui.list_analysis_batch_ref_chains, 7272 self._view.ui.btn_analysis_batch_back_2, 7273 self._view.ui.btn_analysis_batch_next_2, 7274 self._view.ui.box_analysis_batch_prot_struct_1, 7275 self._view.ui.box_analysis_batch_prot_struct_2, 7276 self._view.ui.btn_analysis_batch_back, 7277 self._view.ui.btn_analysis_batch_next, 7278 self._view.ui.lbl_analysis_batch_model_chains, 7279 self._view.ui.list_analysis_batch_model_chains, 7280 self._view.ui.btn_analysis_batch_back_3, 7281 self._view.ui.btn_analysis_batch_next_3, 7282 self._view.ui.lbl_analysis_batch_images, 7283 self._view.ui.cb_analysis_batch_images, 7284 self._view.ui.btn_analysis_batch_start, 7285 ] 7286 gui_utils.show_gui_elements(gui_elements_to_show) 7287 gui_utils.hide_gui_elements(gui_elements_to_hide) 7288 if self._view.ui.list_analysis_batch_overview.count() > 0: 7289 self._view.ui.btn_analysis_batch_remove.show() 7290 self._view.ui.btn_analysis_batch_remove.setEnabled(False) 7291 self._view.ui.btn_analysis_batch_start.show() 7292 self._view.ui.lbl_analysis_batch_images.show() 7293 self._view.ui.cb_analysis_batch_images.show() 7294 7295 def structure_analysis_next_2(self) -> None: 7296 """Shows the gui elements to select the chains in protein 2.""" 7297 gui_elements_to_show = [ 7298 self._view.ui.lbl_analysis_batch_overview, 7299 self._view.ui.list_analysis_batch_overview, 7300 self._view.ui.lbl_analysis_batch_prot_struct_1, 7301 self._view.ui.lbl_analysis_batch_prot_struct_2, 7302 self._view.ui.lbl_analysis_batch_vs, 7303 self._view.ui.lbl_analysis_batch_ref_chains, 7304 self._view.ui.list_analysis_batch_ref_chains, 7305 self._view.ui.lbl_analysis_batch_model_chains, 7306 self._view.ui.list_analysis_batch_model_chains, 7307 self._view.ui.btn_analysis_batch_back_3, 7308 self._view.ui.btn_analysis_batch_next_3, 7309 ] 7310 gui_elements_to_hide = [ 7311 self._view.ui.btn_analysis_batch_remove, 7312 self._view.ui.btn_analysis_batch_add, 7313 self._view.ui.box_analysis_batch_prot_struct_1, 7314 self._view.ui.box_analysis_batch_prot_struct_2, 7315 self._view.ui.btn_analysis_batch_back, 7316 self._view.ui.btn_analysis_batch_next, 7317 self._view.ui.btn_analysis_batch_back_2, 7318 self._view.ui.btn_analysis_batch_next_2, 7319 self._view.ui.lbl_analysis_batch_images, 7320 self._view.ui.cb_analysis_batch_images, 7321 self._view.ui.btn_analysis_batch_start, 7322 ] 7323 gui_utils.show_gui_elements(gui_elements_to_show) 7324 gui_utils.hide_gui_elements(gui_elements_to_hide) 7325 self._view.ui.list_analysis_batch_model_chains.clear() 7326 self._view.ui.list_analysis_batch_ref_chains.setEnabled(False) 7327 self._view.ui.btn_analysis_batch_next_3.setEnabled(False) 7328 7329 tmp_protein = self._current_project.search_protein(self._view.ui.box_analysis_batch_prot_struct_2.currentText()) 7330 for tmp_chain in tmp_protein.chains: 7331 if tmp_chain.chain_type == "protein_chain": 7332 self._view.ui.list_analysis_batch_model_chains.addItem(tmp_chain.chain_letter) 7333 if len(self._view.ui.list_analysis_batch_ref_chains.selectedItems()) == 1: 7334 self._view.ui.lbl_analysis_batch_model_chains.setText( 7335 f"Select 1 chain in protein structure {self._view.ui.lbl_analysis_batch_prot_struct_2.text()}.", 7336 ) 7337 else: 7338 self._view.ui.lbl_analysis_batch_model_chains.setText( 7339 f"Select {len(self._view.ui.list_analysis_batch_ref_chains.selectedItems())} chains in " 7340 f"protein structure {self._view.ui.lbl_analysis_batch_prot_struct_2.text()}.", 7341 ) 7342 7343 def structure_analysis_back_2(self) -> None: 7344 """Hides the gui elements to select the chains in protein 1.""" 7345 gui_elements_to_show = [ 7346 self._view.ui.lbl_analysis_batch_overview, 7347 self._view.ui.list_analysis_batch_overview, 7348 self._view.ui.lbl_analysis_batch_prot_struct_1, 7349 self._view.ui.box_analysis_batch_prot_struct_1, 7350 self._view.ui.lbl_analysis_batch_vs, 7351 self._view.ui.lbl_analysis_batch_prot_struct_2, 7352 self._view.ui.box_analysis_batch_prot_struct_2, 7353 self._view.ui.btn_analysis_batch_back, 7354 self._view.ui.btn_analysis_batch_next, 7355 ] 7356 gui_elements_to_hide = [ 7357 self._view.ui.btn_analysis_batch_remove, 7358 self._view.ui.btn_analysis_batch_add, 7359 self._view.ui.lbl_analysis_batch_ref_chains, 7360 self._view.ui.list_analysis_batch_ref_chains, 7361 self._view.ui.btn_analysis_batch_back_2, 7362 self._view.ui.btn_analysis_batch_next_2, 7363 self._view.ui.lbl_analysis_batch_model_chains, 7364 self._view.ui.list_analysis_batch_model_chains, 7365 self._view.ui.btn_analysis_batch_back_3, 7366 self._view.ui.btn_analysis_batch_next_3, 7367 self._view.ui.lbl_analysis_batch_images, 7368 self._view.ui.cb_analysis_batch_images, 7369 self._view.ui.btn_analysis_batch_start, 7370 ] 7371 gui_utils.show_gui_elements(gui_elements_to_show) 7372 gui_utils.hide_gui_elements(gui_elements_to_hide) 7373 self._view.ui.lbl_analysis_batch_prot_struct_1.setText("Protein structure 1") 7374 self._view.ui.lbl_analysis_batch_prot_struct_2.setText("Protein structure 2") 7375 7376 def structure_analysis_next_3(self) -> None: 7377 """Adds the protein pair to the list of protein pairs to analyze.""" 7378 gui_elements_to_show = [ 7379 self._view.ui.btn_analysis_batch_remove, 7380 self._view.ui.btn_analysis_batch_add, 7381 self._view.ui.lbl_analysis_batch_overview, 7382 self._view.ui.list_analysis_batch_overview, 7383 self._view.ui.lbl_analysis_batch_images, 7384 self._view.ui.cb_analysis_batch_images, 7385 self._view.ui.btn_analysis_batch_start, 7386 ] 7387 gui_elements_to_hide = [ 7388 self._view.ui.box_analysis_batch_prot_struct_1, 7389 self._view.ui.box_analysis_batch_prot_struct_2, 7390 self._view.ui.lbl_analysis_batch_prot_struct_1, 7391 self._view.ui.lbl_analysis_batch_prot_struct_2, 7392 self._view.ui.lbl_analysis_batch_vs, 7393 self._view.ui.lbl_analysis_batch_ref_chains, 7394 self._view.ui.list_analysis_batch_ref_chains, 7395 self._view.ui.lbl_analysis_batch_model_chains, 7396 self._view.ui.list_analysis_batch_model_chains, 7397 self._view.ui.btn_analysis_batch_back, 7398 self._view.ui.btn_analysis_batch_next, 7399 self._view.ui.btn_analysis_batch_back_2, 7400 self._view.ui.btn_analysis_batch_next_2, 7401 self._view.ui.btn_analysis_batch_back_3, 7402 self._view.ui.btn_analysis_batch_next_3, 7403 ] 7404 gui_utils.show_gui_elements(gui_elements_to_show) 7405 gui_utils.hide_gui_elements(gui_elements_to_hide) 7406 prot_1_name = self._view.ui.lbl_analysis_batch_prot_struct_1.text() 7407 prot_1_chains = [] 7408 for chain in self._view.ui.list_analysis_batch_ref_chains.selectedItems(): 7409 prot_1_chains.append(chain.text()) 7410 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 7411 prot_2_name = self._view.ui.lbl_analysis_batch_prot_struct_2.text() 7412 prot_2_chains = [] 7413 for chain in self._view.ui.list_analysis_batch_model_chains.selectedItems(): 7414 prot_2_chains.append(chain.text()) 7415 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 7416 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 7417 item = QtWidgets.QListWidgetItem(analysis_name) 7418 self._view.ui.list_analysis_batch_overview.addItem(item) 7419 self._view.ui.btn_analysis_batch_remove.setEnabled(False) 7420 7421 def structure_analysis_back_3(self) -> None: 7422 """Hides the gui elements to select the chains in protein 2.""" 7423 gui_elements_to_show = [ 7424 self._view.ui.lbl_analysis_batch_overview, 7425 self._view.ui.list_analysis_batch_overview, 7426 self._view.ui.lbl_analysis_batch_prot_struct_1, 7427 self._view.ui.lbl_analysis_batch_prot_struct_2, 7428 self._view.ui.lbl_analysis_batch_vs, 7429 self._view.ui.lbl_analysis_batch_ref_chains, 7430 self._view.ui.list_analysis_batch_ref_chains, 7431 self._view.ui.btn_analysis_batch_back_2, 7432 self._view.ui.btn_analysis_batch_next_2, 7433 ] 7434 gui_elements_to_hide = [ 7435 self._view.ui.btn_analysis_batch_remove, 7436 self._view.ui.btn_analysis_batch_add, 7437 self._view.ui.box_analysis_batch_prot_struct_1, 7438 self._view.ui.box_analysis_batch_prot_struct_2, 7439 self._view.ui.btn_analysis_batch_back, 7440 self._view.ui.btn_analysis_batch_next, 7441 self._view.ui.btn_analysis_batch_back_3, 7442 self._view.ui.btn_analysis_batch_next_3, 7443 self._view.ui.lbl_analysis_batch_images, 7444 self._view.ui.cb_analysis_batch_images, 7445 self._view.ui.btn_analysis_batch_start, 7446 self._view.ui.lbl_analysis_batch_model_chains, 7447 self._view.ui.list_analysis_batch_model_chains, 7448 ] 7449 gui_utils.show_gui_elements(gui_elements_to_show) 7450 gui_utils.hide_gui_elements(gui_elements_to_hide) 7451 self._view.ui.list_analysis_batch_ref_chains.setEnabled(True) 7452 7453 # tmp_protein = self._current_project.search_protein(self._view.ui.box_analysis_batch_prot_struct_2.currentText()) 7454 # for tmp_chain in tmp_protein.chains: 7455 # if tmp_chain.chain_type == "protein_chain": 7456 # self._view.ui.list_analysis_batch_ref_chains.addItem(tmp_chain.chain_letter) 7457 7458 def structure_analysis_overview_clicked(self) -> None: 7459 """Enables the remove button.""" 7460 self._view.ui.btn_analysis_batch_remove.setEnabled(True) 7461 7462 def fill_protein_boxes_batch(self) -> None: 7463 """Fills the combo boxes with the protein names.""" 7464 proteins = [] 7465 for tmp_protein in self._current_project.proteins: 7466 proteins.append(tmp_protein.get_molecule_object()) 7467 proteins.insert(0, "") 7468 self._view.ui.box_analysis_batch_prot_struct_1.clear() 7469 self._view.ui.box_analysis_batch_prot_struct_2.clear() 7470 gui_utils.fill_combo_box(self._view.ui.box_analysis_batch_prot_struct_1, proteins) 7471 gui_utils.fill_combo_box(self._view.ui.box_analysis_batch_prot_struct_2, proteins) 7472 7473 def remove_analysis_run(self) -> None: 7474 """Removes the selected protein pair from the list of protein pairs to analyze.""" 7475 self._view.ui.list_analysis_batch_overview.takeItem(self._view.ui.list_analysis_batch_overview.currentRow()) 7476 if self._view.ui.list_analysis_batch_overview.count() == 0: 7477 gui_elements_to_show = [ 7478 self._view.ui.lbl_analysis_batch_overview, 7479 self._view.ui.list_analysis_batch_overview, 7480 self._view.ui.btn_analysis_batch_add, 7481 ] 7482 7483 gui_elements_to_hide = [ 7484 self._view.ui.btn_analysis_batch_remove, 7485 self._view.ui.lbl_analysis_batch_prot_struct_1, 7486 self._view.ui.lbl_analysis_batch_prot_struct_2, 7487 self._view.ui.lbl_analysis_batch_vs, 7488 self._view.ui.lbl_analysis_batch_ref_chains, 7489 self._view.ui.list_analysis_batch_ref_chains, 7490 self._view.ui.btn_analysis_batch_back_2, 7491 self._view.ui.btn_analysis_batch_next_2, 7492 self._view.ui.box_analysis_batch_prot_struct_1, 7493 self._view.ui.box_analysis_batch_prot_struct_2, 7494 self._view.ui.btn_analysis_batch_back, 7495 self._view.ui.btn_analysis_batch_next, 7496 self._view.ui.lbl_analysis_batch_model_chains, 7497 self._view.ui.list_analysis_batch_model_chains, 7498 self._view.ui.btn_analysis_batch_back_3, 7499 self._view.ui.btn_analysis_batch_next_3, 7500 self._view.ui.lbl_analysis_batch_images, 7501 self._view.ui.cb_analysis_batch_images, 7502 self._view.ui.btn_analysis_batch_start, 7503 ] 7504 7505 gui_utils.show_gui_elements(gui_elements_to_show) 7506 gui_utils.hide_gui_elements(gui_elements_to_hide) 7507 self._view.ui.btn_analysis_batch_remove.hide() 7508 else: 7509 if self._view.ui.list_analysis_batch_overview.count() > 0: 7510 try: 7511 self._view.ui.list_analysis_batch_overview.currentItem().setSelected(False) 7512 except AttributeError: 7513 constants.PYSSA_LOGGER.debug("No selection in struction analysis overview.") 7514 self._view.ui.btn_analysis_batch_remove.setEnabled(False) 7515 7516 def check_if_same_no_of_chains_selected_batch(self) -> None: 7517 """Checks if the same number of proteins were selected.""" 7518 self._view.ui.btn_analysis_batch_next_3.setEnabled(False) 7519 if self.no_of_selected_chains == len(self._view.ui.list_analysis_batch_model_chains.selectedItems()): 7520 self._view.ui.btn_analysis_batch_next_3.setEnabled(True) 7521 7522 prot_1_name = self._view.ui.lbl_analysis_batch_prot_struct_1.text() 7523 prot_1_chains = [] 7524 for chain in self._view.ui.list_analysis_batch_ref_chains.selectedItems(): 7525 prot_1_chains.append(chain.text()) 7526 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 7527 prot_2_name = self._view.ui.lbl_analysis_batch_prot_struct_2.text() 7528 prot_2_chains = [] 7529 for chain in self._view.ui.list_analysis_batch_model_chains.selectedItems(): 7530 prot_2_chains.append(chain.text()) 7531 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 7532 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 7533 for tmp_row in range(self._view.ui.list_analysis_batch_overview.count()): 7534 if analysis_name == self._view.ui.list_analysis_batch_overview.item(tmp_row).text(): 7535 self._view.ui.btn_analysis_batch_next_3.setEnabled(False) 7536 styles.color_button_not_ready(self._view.ui.btn_analysis_batch_next_3) 7537 return 7538 7539 def check_if_prot_structs_are_filled_batch(self) -> None: 7540 """Checks if two proteins were selected.""" 7541 prot_1 = self._view.ui.box_analysis_batch_prot_struct_1.itemText( 7542 self._view.ui.box_analysis_batch_prot_struct_1.currentIndex(), 7543 ) 7544 prot_2 = self._view.ui.box_analysis_batch_prot_struct_2.itemText( 7545 self._view.ui.box_analysis_batch_prot_struct_2.currentIndex(), 7546 ) 7547 if prot_1 != "" and prot_2 != "": 7548 self._view.ui.btn_analysis_batch_next.setEnabled(True) 7549 else: 7550 self._view.ui.btn_analysis_batch_next.setEnabled(False) 7551 7552 def count_batch_selected_chains_for_prot_struct_1(self) -> None: 7553 """Counts the number of chains of protein 1.""" 7554 self.no_of_selected_chains = len(self._view.ui.list_analysis_batch_ref_chains.selectedItems()) 7555 if self.no_of_selected_chains > 0: 7556 self._view.ui.btn_analysis_batch_next_2.setEnabled(True) 7557 else: 7558 self._view.ui.btn_analysis_batch_next_2.setEnabled(False) 7559 7560 # </editor-fold> 7561 7562 # <editor-fold desc="Analysis images"> 7563 def display_image_analysis_page(self) -> None: 7564 """Displays the analysis image work area.""" 7565 # get all protein pairs without images 7566 self._view.ui.list_analysis_images_struct_analysis.clear() 7567 self._view.ui.list_analysis_images_creation_struct_analysis.clear() 7568 for tmp_protein_pair in self._current_project.protein_pairs: 7569 if len(tmp_protein_pair.distance_analysis.analysis_results.structure_aln_image) == 0: 7570 self._view.ui.list_analysis_images_struct_analysis.addItem(tmp_protein_pair.name) 7571 self.last_sidebar_button = styles.color_sidebar_buttons( 7572 self.last_sidebar_button, 7573 self._view.ui.btn_image_analysis_page, 7574 ) 7575 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 23, "Analysis Images") 7576 self._view.ui.btn_add_analysis_images_struct_analysis.setEnabled(False) 7577 self._view.ui.btn_remove_analysis_images_creation_struct_analysis.setEnabled(False) 7578 self._view.ui.btn_start_automatic_image_creation.setEnabled(False) 7579 7580 def analysis_images_enable_add(self) -> None: 7581 """Enables the add button.""" 7582 self._view.ui.btn_add_analysis_images_struct_analysis.setEnabled(True) 7583 7584 def analysis_images_enable_remove(self) -> None: 7585 """Enables the remove button.""" 7586 self._view.ui.btn_remove_analysis_images_creation_struct_analysis.setEnabled(True) 7587 7588 def add_protein_pair_to_image_creation_queue(self) -> None: 7589 """Adds a protein pair from the list of protein pairs to make images of.""" 7590 protein_pair_to_add = self._view.ui.list_analysis_images_struct_analysis.currentItem().text() 7591 self._view.ui.list_analysis_images_creation_struct_analysis.addItem(protein_pair_to_add) 7592 self._view.ui.list_analysis_images_struct_analysis.takeItem( 7593 self._view.ui.list_analysis_images_struct_analysis.currentRow(), 7594 ) 7595 self._view.ui.btn_add_analysis_images_struct_analysis.setEnabled(False) 7596 self.analysis_images_check_if_creation_can_start() 7597 7598 def remove_protein_pair_from_image_creation_queue(self) -> None: 7599 """Removes a protein pair from the list of protein pairs to make images of.""" 7600 protein_pair_to_remove = self._view.ui.list_analysis_images_creation_struct_analysis.currentItem() 7601 self._view.ui.list_analysis_images_creation_struct_analysis.takeItem( 7602 self._view.ui.list_analysis_images_creation_struct_analysis.currentRow(), 7603 ) 7604 self._view.ui.list_analysis_images_struct_analysis.addItem(protein_pair_to_remove) 7605 self._view.ui.btn_remove_analysis_images_creation_struct_analysis.setEnabled(False) 7606 self.analysis_images_check_if_creation_can_start() 7607 7608 def analysis_images_check_if_creation_can_start(self) -> None: 7609 """Checks if the list of protein pairs which get images are empty.""" 7610 if self._view.ui.list_analysis_images_creation_struct_analysis.count() > 0: 7611 self._view.ui.btn_start_automatic_image_creation.setEnabled(True) 7612 else: 7613 self._view.ui.btn_start_automatic_image_creation.setEnabled(False) 7614 7615 # </editor-fold> 7616 7617 # </editor-fold> 7618 7619 def update_status(self, message: str) -> None: 7620 """Updates the status bar of the main view with a custom message.""" 7621 self._view.status_bar.showMessage(message)
logger =
<Logger C:\Users\martin\github_repos\PySSA\pyssa\presenter\main_presenter.py (DEBUG)>
class
MainPresenter:
90class MainPresenter: 91 """Class for main presenter of the pyssa plugin.""" 92 93 """ 94 The main view of the pyssa plugin. 95 """ 96 _view: "main_view.MainView" 97 98 """ 99 The path to the active workspace. 100 """ 101 _workspace_path: pathlib.Path 102 103 """ 104 The application settings object. 105 """ 106 _application_settings: "settings.Settings" 107 108 """ 109 The currently active project. 110 """ 111 _current_project: "project.Project" 112 113 """ 114 A watcher for the project state. 115 """ 116 _project_watcher: "project_watcher.ProjectWatcher" 117 118 """ 119 The active task of the application. 120 """ 121 _active_task: tasks.Task 122 123 def __init__(self, a_view: "main_view.MainView") -> None: 124 """Constructor. 125 126 Args: 127 a_view: the main view of the pyssa plugin. 128 129 Raises: 130 IllegalArgumentException: If an argument is illegal. 131 """ 132 # <editor-fold desc="Checks"> 133 safeguard.Safeguard.check_if_value_is_not_none(a_view, logger) 134 135 # </editor-fold> 136 137 # <editor-fold desc="Initialize class attributes"> 138 self._view = a_view 139 self._workspace_path = constants.DEFAULT_WORKSPACE_PATH 140 # TODO: settings and project objects get not initialized properly 141 self._application_settings = settings.Settings("", "") 142 self._current_project: "project.Project" = project.Project() 143 self._project_watcher: "project_watcher.ProjectWatcher" = project_watcher.ProjectWatcher(self._current_project) 144 145 # </editor-fold> 146 147 # Check OS 148 main_window_util.check_operating_system() 149 # Create log dir 150 # <editor-fold desc="Program directory check"> 151 filesystem_helpers.create_directory(pathlib.Path(f"{os.path.expanduser('~')}/.pyssa")) 152 filesystem_helpers.create_directory(pathlib.Path(f"{os.path.expanduser('~')}/.pyssa/logs")) 153 constants.PYSSA_LOGGER.info("Checked program and logs directory.") 154 155 # </editor-fold> 156 # Configure settings 157 # <editor-fold desc="Setup App Settings"> 158 self._application_settings = settings.Settings(constants.SETTINGS_DIR, constants.SETTINGS_FILENAME) 159 if not os.path.exists(constants.SETTINGS_FULL_FILEPATH): 160 constants.PYSSA_LOGGER.info("Settings file not found, open configuration dialog.") 161 # Configuration dialog to setup setting file 162 dialog = dialog_startup.DialogStartup() 163 dialog.exec_() 164 165 # checks if the cancel button was pressed 166 if dialog_startup.global_var_terminate_app == 1: 167 os.remove(constants.SETTINGS_FULL_FILEPATH) 168 constants.PYSSA_LOGGER.info("Configuration dialog closed, and removed new settings file.") 169 sys.exit() 170 171 self._application_settings.app_launch = 1 172 self._application_settings.workspace_path = pathlib.Path(dialog_startup.global_var_startup_workspace) 173 174 constants.PYSSA_LOGGER.info("Demo projects are getting downloaded and extracted ...") 175 import zipfile 176 177 with zipfile.ZipFile(pathlib.Path(f"{constants.SETTINGS_DIR}/demo-projects.zip"), "r") as zip_ref: 178 zip_ref.extractall(pathlib.Path(f"{constants.SETTINGS_DIR}/demo-projects")) 179 constants.PYSSA_LOGGER.info( 180 "Demo projects are downloaded and extracted.\n Import of demo projects started ...", 181 ) 182 183 path_of_demo_projects = pathlib.Path(f"{constants.SETTINGS_DIR}/demo-projects") 184 tmp_project = project.Project("", dialog_startup.global_var_startup_workspace) 185 for tmp_filename in os.listdir(path_of_demo_projects): 186 try: 187 tmp_project = tmp_project.deserialize_project( 188 pathlib.Path(f"{path_of_demo_projects}/{tmp_filename}"), 189 self._application_settings, 190 ) 191 except exception.IllegalArgumentError: 192 constants.PYSSA_LOGGER.warning( 193 "The workspace path does not exist on this system, " "but this is due to the demo projects.", 194 ) 195 tmp_project.set_workspace_path(dialog_startup.global_var_startup_workspace) 196 new_filepath = pathlib.Path(f"{dialog_startup.global_var_startup_workspace}/{tmp_filename}") 197 tmp_project.serialize_project(new_filepath) 198 constants.PYSSA_LOGGER.info("Import process of demo projects finished.") 199 try: 200 os.remove(pathlib.Path(f"{constants.SETTINGS_DIR}/demo-projects.zip")) 201 except FileNotFoundError: 202 constants.PYSSA_LOGGER.warning("Zip archive of demo projects could not be found!") 203 constants.PYSSA_LOGGER.info("Serialize settings ...") 204 self._application_settings.serialize_settings() 205 constants.PYSSA_LOGGER.info("Serialize settings finished.") 206 207 QtWidgets.QApplication.restoreOverrideCursor() 208 209 globals.g_settings = main_window_util.setup_app_settings(self._application_settings) 210 self._application_settings = globals.g_settings 211 # </editor-fold> 212 # Check version number 213 main_window_util.check_version_number() 214 215 # <editor-fold desc="Class attributes"> 216 self._workspace_path = self._application_settings.workspace_path 217 self._workspace_status = f"Current workspace: {str(self._workspace_path)}" 218 self._workspace_label = QtWidgets.QLabel(f"Current Workspace: {self._workspace_path}") 219 self.prediction_configuration = prediction_configuration.PredictionConfiguration(True, "pdb70") 220 self.results_name = "" 221 self.no_of_selected_chains = 0 222 self.plot_dialog = QtWidgets.QDialog(self._view) 223 self.view_box = None 224 self.block_box_expert_install = basic_boxes.no_buttons( 225 "Local Colabfold installation", 226 "An installation process is currently running.", 227 QtWidgets.QMessageBox.Information, 228 ) 229 self.prediction_type = 0 230 self.current_session = current_session.CurrentSession("", "", "") 231 self.is_distance_plot_open = False 232 self.distance_plot_dialog = None 233 234 self.main_window_state = main_window_state.MainWindowState( 235 results_state.ResultsState(), 236 image_state.ImageState(), 237 ) 238 239 constants.PYSSA_LOGGER.info("Setup class attributes finished.") 240 # </editor-fold> 241 242 # sets up the status bar 243 self._setup_statusbar() 244 tools.create_directory(constants.SETTINGS_DIR, "scratch") 245 self._setup_default_configuration() 246 247 # if len(os.listdir(constants.LOG_PATH)) > 0: 248 # self.open_change_log() 249 250 constants.PYSSA_LOGGER.info("Setup rest of GUI related elements ...") 251 252 # <editor-fold desc="GUI page management"> 253 # -- Gui page management vars 254 self.batch_analysis_management: gui_page_management.GuiPageManagement 255 self.results_management: gui_page_management.GuiPageManagement 256 257 # management functions 258 self._create_batch_analysis_management() 259 self._create_results_management() 260 261 # </editor-fold> 262 263 # <editor-fold desc="Block box definitions"> 264 self.block_box_analysis = basic_boxes.no_buttons( 265 "Analysis", 266 "An analysis is currently running, please wait.", 267 QtWidgets.QMessageBox.Information, 268 ) 269 self.block_box_prediction: QtWidgets.QMessageBox = QtWidgets.QMessageBox() 270 self.block_box_images = basic_boxes.no_buttons( 271 "Analysis Images", 272 "Images getting created, please wait.", 273 QtWidgets.QMessageBox.Information, 274 ) 275 self.block_box_uni = basic_boxes.no_buttons("Generic", "Generic", QtWidgets.QMessageBox.Information) 276 277 # </editor-fold> 278 279 # configure gui element properties 280 self._view.ui.txt_results_aligned_residues.setAlignment(QtCore.Qt.AlignRight) 281 self._view.ui.table_pred_mono_prot_to_predict.setSizeAdjustPolicy( 282 QtWidgets.QAbstractScrollArea.AdjustToContents, 283 ) 284 self._view.ui.table_pred_mono_prot_to_predict.horizontalHeader().setDefaultAlignment(QtCore.Qt.AlignLeft) 285 self._view.ui.table_pred_multi_prot_to_predict.horizontalHeader().setDefaultAlignment(QtCore.Qt.AlignLeft) 286 self._view.ui.list_pred_analysis_multi_ref_chains.setSelectionMode( 287 QtWidgets.QAbstractItemView.ExtendedSelection, 288 ) 289 self._view.ui.list_pred_analysis_multi_model_chains.setSelectionMode( 290 QtWidgets.QAbstractItemView.ExtendedSelection, 291 ) 292 293 # helper attributes 294 self.pymol_session_specs = { 295 pyssa_keys.SESSION_SPEC_PROTEIN: [0, ""], 296 pyssa_keys.SESSION_SPEC_COLOR: [0, ""], 297 pyssa_keys.SESSION_SPEC_REPRESENTATION: [0, ""], 298 pyssa_keys.SESSION_SPEC_BG_COLOR: [0, ""], 299 } 300 301 # <editor-fold desc="Setup defaults for pages"> 302 self._init_fill_combo_boxes() 303 self._init_new_page() 304 self._init_use_page() 305 self._init_local_pred_mono_page() 306 self._init_local_pred_multi_page() 307 self._init_batch_analysis_page() 308 self._view.ui.action_toggle_notebook_visibility.setVisible(False) 309 self._view.ui.action_settings_model_w_off_colab_notebook.setVisible(False) 310 self.last_sidebar_button = QtWidgets.QPushButton() 311 self._view.ui.table_pred_mono_prot_to_predict.setEditTriggers( 312 self._view.ui.table_pred_mono_prot_to_predict.NoEditTriggers, 313 ) 314 self._view.ui.table_pred_multi_prot_to_predict.setEditTriggers( 315 self._view.ui.table_pred_multi_prot_to_predict.NoEditTriggers, 316 ) 317 self._view.ui.table_pred_analysis_mono_prot_to_predict.setEditTriggers( 318 self._view.ui.table_pred_analysis_mono_prot_to_predict.NoEditTriggers, 319 ) 320 self._view.ui.table_pred_analysis_multi_prot_to_predict.setEditTriggers( 321 self._view.ui.table_pred_analysis_multi_prot_to_predict.NoEditTriggers, 322 ) 323 324 # TODO: temp gui changes (need to be changed in the designer) 325 self._view.ui.lbl_hotspots_resi_show.setText("Residue(s) as sticks") 326 self._view.ui.lbl_hotspots_resi_hide.setText("Residue(s) as sticks") 327 328 # fixme: should the pdf documentation be accessible through the pyssa gui? 329 self._view.ui.action_help_docs_pdf.setText("Documentation") 330 self._view.ui.action_help_docs_pdf.setVisible(True) 331 self._view.ui.action_help_docs.setText("Tutorials") 332 self._view.ui.action_help_docs.setVisible(True) 333 334 if self._application_settings.wsl_install == 1 and self._application_settings.local_colabfold == 0: 335 self._view.ui.action_install_from_file.setVisible(True) 336 else: 337 self._view.ui.action_install_from_file.setVisible(False) 338 # </editor-fold> 339 340 self._connect_all_gui_elements() 341 342 self._project_watcher.show_valid_options(self._view.ui) 343 self._project_watcher.check_workspace_for_projects(self._workspace_path, self._view.ui) 344 345 self.threadpool = QtCore.QThreadPool() 346 # create scratch and cache dir 347 try: 348 filesystem_helpers.delete_directory(constants.SCRATCH_DIR) 349 except Exception as e: 350 constants.PYSSA_LOGGER.warning(f"Scratch path could not be deleted. {e}") 351 filesystem_helpers.create_directory(constants.SCRATCH_DIR) 352 filesystem_helpers.create_directory(constants.CACHE_DIR) 353 354 def start_worker_thread(self, worker_obj: object, post_process_func) -> None: # noqa: ANN001 355 """Sets up the worker, moves the worker to a thread and starts the thread. 356 357 Args: 358 worker_obj: an object of type <work>Worker (QObject). 359 post_process_func: a function which sould be executed if the worker is finished. 360 """ 361 self.tmp_thread = QtCore.QThread() 362 self.tmp_worker = worker_obj 363 self.tmp_thread = task_workers.setup_worker_for_work(self.tmp_thread, self.tmp_worker, post_process_func) 364 self.tmp_thread.start() 365 366 def _setup_statusbar(self) -> None: 367 """Sets up the status bar and fills it with the current workspace.""" 368 self._view.setStatusBar(self._view.status_bar) 369 self._view.status_bar.showMessage(str(self._workspace_label.text())) 370 371 def _setup_default_configuration(self) -> None: 372 """Sets up the default values for specific gui elements.""" 373 self._view.ui.lbl_current_project_name.setText("") 374 # menu 375 # side menu 376 377 # new project page 378 self._view.ui.btn_new_create_project.setEnabled(False) 379 self._view.ui.cb_new_add_reference.setCheckable(False) 380 self._view.ui.cb_new_add_reference.setStyleSheet("color: #E1E1E1;") 381 # open project page 382 self._view.ui.lbl_open_status_search.setText("") 383 self._view.ui.btn_open_open_project.setEnabled(False) 384 # delete project page 385 self._view.ui.lbl_delete_status_search.setText("") 386 self._view.ui.btn_delete_delete_project.setEnabled(False) 387 # edit project page 388 389 # view project page 390 391 # use project page 392 393 # new sequence page 394 # sequence vs .pdb page 395 self._view.ui.btn_s_v_p_start.setEnabled(False) 396 self._view.ui.list_s_v_p_ref_chains.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection) 397 # single analysis page 398 self._view.ui.lbl_analysis_model_chains.hide() 399 self._view.ui.list_analysis_model_chains.hide() 400 self._view.ui.btn_analysis_back.hide() 401 self._view.ui.btn_analysis_start.hide() 402 # batch analysis page 403 404 # results page 405 406 # image page 407 408 def _connect_all_gui_elements(self) -> None: 409 """Connects all gui elements with their corresponding slots.""" 410 self._view.ui.btn_info.clicked.connect(self.open_page_information) 411 412 # <editor-fold desc="Menu"> 413 self._view.ui.action_file_quit.triggered.connect(self.quit_app) 414 self._view.ui.action_file_restore_settings.triggered.connect(self.restore_settings) 415 self._view.ui.action_settings_edit_all.triggered.connect(self.open_settings_global) 416 self._view.ui.action_help_docs.triggered.connect(self.open_tutorial) 417 self._view.ui.action_help_docs_pdf.triggered.connect(self.open_documentation) 418 self._view.ui.action_help_about.triggered.connect(self.open_about) 419 self._view.ui.action_settings_open_logs.triggered.connect(self.open_logs) 420 self._view.ui.action_settings_clear_logs.triggered.connect(self.clear_all_log_files) 421 self._view.ui.action_help_changelog.triggered.connect(self.open_release_notes_in_standard_application) 422 # </editor-fold> 423 424 # <editor-fold desc="Side Menu"> 425 self._view.ui.btn_new_page.clicked.connect(self.display_new_page) 426 self._view.ui.btn_open_page.clicked.connect(self.display_open_page) 427 self._view.ui.btn_delete_page.clicked.connect(self.display_delete_page) 428 self._view.ui.btn_save_project.clicked.connect(self.save_project) 429 self._view.ui.btn_edit_page.clicked.connect(self.display_edit_page) 430 self._view.ui.btn_view_page.clicked.connect(self.display_view_page) 431 self._view.ui.btn_use_page.clicked.connect(self.display_use_page) 432 self._view.ui.btn_import_project.clicked.connect(self.import_project) 433 self._view.ui.btn_export_project.clicked.connect(self.export_current_project) 434 self._view.ui.btn_close_project.clicked.connect(self.close_project) 435 self._view.ui.btn_pred_cloud_monomer_page.clicked.connect(self.display_esm_pred_mono) 436 self._view.ui.btn_pred_local_monomer_page.clicked.connect(self.display_local_pred_mono) 437 self._view.ui.btn_pred_local_multimer_page.clicked.connect(self.display_local_pred_multi) 438 self._view.ui.btn_prediction_abort.clicked.connect(self.abort_prediction) 439 self._view.ui.btn_pred_analysis_monomer_page.clicked.connect(self.display_monomer_pred_analysis) 440 self._view.ui.btn_pred_analysis_multimer_page.clicked.connect(self.display_multimer_pred_analysis) 441 self._view.ui.btn_batch_analysis_page.clicked.connect(self.display_job_analysis_page) 442 self._view.ui.btn_image_analysis_page.clicked.connect(self.display_image_analysis_page) 443 self._view.ui.btn_results_page.clicked.connect(self.display_results_page) 444 # self._view.ui.btn_analysis_abort.clicked.connect(self.abort_analysis) 445 self._view.ui.btn_manage_session.clicked.connect(self.display_manage_pymol_session) 446 self._view.ui.btn_image_page.clicked.connect(self.display_image_page) 447 self._view.ui.btn_hotspots_page.clicked.connect(self.display_hotspots_page) 448 449 # </editor-fold> 450 451 # <editor-fold desc="New project page"> 452 self._view.ui.btn_new_choose_reference.clicked.connect(self.load_reference_in_project) 453 self._view.ui.txt_new_project_name.textChanged.connect(self.validate_project_name) 454 self._view.ui.txt_new_choose_reference.textChanged.connect(self.validate_reference_in_project) 455 self._view.ui.cb_new_add_reference.stateChanged.connect(self.show_add_reference) 456 self._view.ui.btn_new_create_project.clicked.connect(self.create_new_project) 457 458 # </editor-fold> 459 460 # <editor-fold desc="Open project page"> 461 self._view.ui.btn_open_open_project.clicked.connect(self.open_project) 462 self._view.ui.list_open_projects.doubleClicked.connect(self.open_project) 463 self._view.ui.txt_open_search.textChanged.connect(self.validate_open_search) 464 self._view.ui.txt_open_selected_project.textChanged.connect(self.activate_open_button) 465 self._view.ui.list_open_projects.currentItemChanged.connect(self.select_project_from_open_list) 466 467 # </editor-fold> 468 469 # <editor-fold desc="Delete project page"> 470 self._view.ui.btn_delete_delete_project.clicked.connect(self.delete_project) 471 self._view.ui.txt_delete_search.textChanged.connect(self.validate_delete_search) 472 self._view.ui.txt_delete_selected_projects.textChanged.connect(self.activate_delete_button) 473 self._view.ui.list_delete_projects.currentItemChanged.connect(self.select_project_from_delete_list) 474 475 # </editor-fold> 476 477 # <editor-fold desc="Edit project page"> 478 self._view.ui.btn_edit_page.clicked.connect(self.display_edit_page) 479 self._view.ui.list_edit_project_proteins.currentItemChanged.connect(self.check_for_cleaning) 480 self._view.ui.btn_edit_clean_new_prot.clicked.connect(self.clean_protein_new) 481 self._view.ui.btn_edit_clean_update_prot.clicked.connect(self.clean_protein_update) 482 self._view.ui.btn_edit_project_delete.clicked.connect(self.delete_protein) 483 self._view.ui.btn_edit_existing_protein_struct.clicked.connect(self.add_existing_protein) 484 self._view.ui.btn_edit_project_save.clicked.connect(self.save_selected_protein_structure_as_pdb_file) 485 self._view.ui.btn_edit_protein_rename.clicked.connect(self.rename_selected_protein_structure) 486 # </editor-fold> 487 488 # <editor-fold desc="View project page"> 489 self._view.ui.btn_view_project_show.clicked.connect(self.view_sequence) 490 self._view.ui.btn_view_project_show_structure.clicked.connect(self.view_structure) 491 self._view.ui.list_view_project_proteins.doubleClicked.connect(self.view_sequence) 492 self._view.ui.list_view_project_proteins.itemClicked.connect(self.view_show_options) 493 # </editor-fold> 494 495 # <editor-fold desc="Use project page"> 496 self._view.ui.txt_use_project_name.textChanged.connect(self.validate_use_project_name) 497 self._view.ui.btn_use_next.clicked.connect(self.show_protein_selection_for_use) 498 self._view.ui.txt_use_search.textChanged.connect(self.validate_use_search) 499 self._view.ui.btn_use_add_available_protein_structures.clicked.connect( 500 self.add_protein_structure_to_new_project, 501 ) 502 self._view.ui.list_use_available_protein_structures.doubleClicked.connect( 503 self.add_protein_structure_to_new_project, 504 ) 505 self._view.ui.list_use_available_protein_structures.itemClicked.connect(self.use_enable_add) 506 self._view.ui.btn_use_remove_selected_protein_structures.clicked.connect( 507 self.remove_protein_structure_to_new_project, 508 ) 509 self._view.ui.list_use_selected_protein_structures.doubleClicked.connect( 510 self.remove_protein_structure_to_new_project, 511 ) 512 self._view.ui.list_use_selected_protein_structures.itemClicked.connect(self.use_enable_remove) 513 self._view.ui.btn_use_back.clicked.connect(self.hide_protein_selection_for_use) 514 self._view.ui.btn_use_create_new_project.clicked.connect(self.pre_create_use_project) 515 516 # </editor-fold> 517 518 # <editor-fold desc="ESMFold Monomer Prediction page"> 519 self._view.ui.btn_esm_seq_to_predict.clicked.connect(self.cloud_esm_add_seq_to_predict) 520 self._view.ui.btn_esm_seq_to_predict_remove.clicked.connect(self.cloud_esm_remove) 521 self._view.ui.btn_esm_next.clicked.connect(self.cloud_esm_next) 522 self._view.ui.btn_esm_back.clicked.connect(self.cloud_esm_back) 523 self._view.ui.btn_esm_next_2.clicked.connect(self.cloud_esm_add_protein) 524 self._view.ui.btn_esm_back_2.clicked.connect(self.cloud_esm_back_2) 525 self._view.ui.txt_esm_prot_name.textChanged.connect(self.cloud_esm_validate_protein_name) 526 self._view.ui.txt_esm_prot_seq.textChanged.connect(self.cloud_esm_validate_protein_sequence) 527 self._view.ui.btn_esm_predict.clicked.connect(self.predict_esm_monomer) 528 529 self._view.ui.table_esm_prot_to_predict.itemSelectionChanged.connect(self.cloud_esm_item_changed) 530 # </editor-fold> 531 532 # <editor-fold desc="Monomer local prediction page"> 533 self._view.ui.btn_pred_mono_seq_to_predict.clicked.connect(self.local_pred_mono_add_seq_to_predict) 534 self._view.ui.btn_pred_mono_seq_to_predict_remove.clicked.connect(self.local_pred_mono_remove) 535 self._view.ui.btn_pred_mono_next.clicked.connect(self.local_pred_mono_next) 536 self._view.ui.btn_pred_mono_back.clicked.connect(self.local_pred_mono_back) 537 self._view.ui.btn_pred_mono_add_protein.clicked.connect(self.local_pred_mono_add_protein) 538 self._view.ui.btn_pred_mono_back_2.clicked.connect(self.local_pred_mono_back_2) 539 self._view.ui.txt_pred_mono_prot_name.textChanged.connect(self.local_pred_mono_validate_protein_name) 540 self._view.ui.txt_pred_mono_seq_name.textChanged.connect(self.local_pred_mono_validate_protein_sequence) 541 self._view.ui.btn_pred_mono_advanced_config.clicked.connect(self.show_prediction_configuration) 542 self._view.ui.btn_pred_mono_predict.clicked.connect(self.predict_local_monomer) 543 544 self._view.ui.table_pred_mono_prot_to_predict.itemSelectionChanged.connect(self.local_pred_mono_item_changed) 545 # </editor-fold> 546 547 # <editor-fold desc="Multimer prediction page"> 548 self._view.ui.btn_pred_multi_prot_to_predict_add.clicked.connect(self.local_pred_multi_add) 549 self._view.ui.btn_pred_multi_prot_to_predict_remove.clicked.connect(self.local_pred_multi_remove) 550 self._view.ui.btn_pred_multi_next.clicked.connect(self.local_pred_multi_next) 551 self._view.ui.btn_pred_multi_back.clicked.connect(self.local_pred_multi_back) 552 self._view.ui.btn_pred_multi_prot_to_predict_add_2.clicked.connect(self.local_pred_multi_prot_to_predict_add_2) 553 self._view.ui.btn_pred_multi_back_2.clicked.connect(self.local_pred_multi_back_2) 554 self._view.ui.txt_pred_multi_prot_name.textChanged.connect(self.local_pred_multi_validate_protein_name) 555 self._view.ui.txt_pred_multi_prot_seq.textChanged.connect(self.local_pred_multi_validate_protein_sequence) 556 self._view.ui.btn_pred_multi_prot_seq_add.clicked.connect(self.local_pred_multi_add_sequence_to_list) 557 self._view.ui.btn_pred_multi_prot_seq_overview_remove.clicked.connect( 558 self.local_pred_multi_remove_sequence_to_list, 559 ) 560 self._view.ui.btn_pred_multi_advanced_config.clicked.connect(self.show_prediction_configuration) 561 self._view.ui.btn_pred_multi_predict.clicked.connect(self.predict_local_multimer) 562 563 self._view.ui.list_pred_multi_prot_seq_overview.itemClicked.connect( 564 self.local_pred_multi_prot_seq_overview_item_changed, 565 ) 566 self._view.ui.table_pred_multi_prot_to_predict.itemSelectionChanged.connect( 567 self.local_pred_multi_prot_to_predict_item_changed, 568 ) 569 # </editor-fold> 570 571 # <editor-fold desc="Monomer Prediction + Analysis page"> 572 # <editor-fold desc="Prediction section"> 573 self._view.ui.btn_pred_analysis_mono_seq_to_predict.clicked.connect(self.mono_pred_analysis_add_seq_to_predict) 574 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.clicked.connect( 575 self.mono_pred_analysis_remove_protein_to_predict, 576 ) 577 self._view.ui.btn_pred_analysis_mono_next.clicked.connect(self.mono_pred_analysis_next) 578 self._view.ui.btn_pred_analysis_mono_back.clicked.connect(self.mono_pred_analysis_back) 579 self._view.ui.btn_pred_analysis_mono_add_protein.clicked.connect(self.mono_pred_analysis_add_protein) 580 self._view.ui.btn_pred_analysis_mono_back_2.clicked.connect(self.mono_pred_analysis_back_2) 581 self._view.ui.txt_pred_analysis_mono_prot_name.textChanged.connect( 582 self.mono_pred_analysis_validate_protein_name, 583 ) 584 self._view.ui.txt_pred_analysis_mono_seq_name.textChanged.connect( 585 self.mono_pred_analysis_validate_protein_sequence, 586 ) 587 self._view.ui.btn_pred_mono_advanced_config_2.clicked.connect(self.show_prediction_configuration) 588 self._view.ui.btn_pred_analysis_mono_go_analysis_setup.clicked.connect(self.switch_monomer_pred_analysis_tab) 589 self._view.ui.table_pred_analysis_mono_prot_to_predict.itemSelectionChanged.connect( 590 self.mono_pred_analysis_prediction_overview_item_clicked, 591 ) 592 593 # </editor-fold> 594 595 # <editor-fold desc="Analysis section"> 596 self._view.ui.btn_pred_analysis_mono_add.clicked.connect(self.mono_pred_analysis_structure_analysis_add) 597 self._view.ui.btn_pred_analysis_mono_remove.clicked.connect(self.remove_mono_pred_analysis_analysis_run) 598 self._view.ui.btn_pred_analysis_mono_back_3.clicked.connect(self.mono_pred_analysis_structure_analysis_back_3) 599 self._view.ui.btn_pred_analysis_mono_next_2.clicked.connect(self.mono_pred_analysis_structure_analysis_next_2) 600 self._view.ui.btn_pred_analysis_mono_back_4.clicked.connect(self.mono_pred_analysis_structure_analysis_back_4) 601 self._view.ui.btn_pred_analysis_mono_next_3.clicked.connect(self.mono_pred_analysis_structure_analysis_next_3) 602 self._view.ui.btn_pred_analysis_mono_back_5.clicked.connect(self.mono_pred_analysis_structure_analysis_back_5) 603 self._view.ui.btn_pred_analysis_mono_next_4.clicked.connect(self.mono_pred_analysis_structure_analysis_next_4) 604 self._view.ui.box_pred_analysis_mono_prot_struct_1.currentIndexChanged.connect( 605 self.check_mono_pred_analysis_if_prot_structs_are_filled, 606 ) 607 self._view.ui.box_pred_analysis_mono_prot_struct_2.currentIndexChanged.connect( 608 self.check_mono_pred_analysis_if_prot_structs_are_filled, 609 ) 610 self._view.ui.list_pred_analysis_mono_ref_chains.itemSelectionChanged.connect( 611 self.count_mono_pred_analysis_selected_chains_for_prot_struct_1, 612 ) 613 self._view.ui.list_pred_analysis_mono_model_chains.itemSelectionChanged.connect( 614 self.check_mono_pred_analysis_if_same_no_of_chains_selected, 615 ) 616 self._view.ui.btn_pred_analysis_mono_back_pred_setup.clicked.connect(self.switch_monomer_pred_analysis_tab) 617 self._view.ui.btn_pred_analysis_mono_start.clicked.connect(self.start_monomer_prediction_analysis) 618 self._view.ui.list_pred_analysis_mono_overview.clicked.connect( 619 self.mono_pred_analysis_structure_analysis_overview_clicked, 620 ) 621 622 # </editor-fold> 623 624 # </editor-fold> 625 626 # <editor-fold desc="Multimer Prediction + Analysis page"> 627 # <editor-fold desc="Prediction section"> 628 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add.clicked.connect(self.multi_pred_analysis_add) 629 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove.clicked.connect( 630 self.multi_pred_analysis_remove_protein_to_predict, 631 ) 632 self._view.ui.btn_pred_analysis_multi_next.clicked.connect(self.multi_pred_analysis_next) 633 self._view.ui.btn_pred_analysis_multi_back.clicked.connect(self.multi_pred_analysis_back) 634 self._view.ui.btn_pred_analysis_multi_prot_seq_add.clicked.connect( 635 self.multi_pred_analysis_add_sequence_to_list, 636 ) 637 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove.clicked.connect( 638 self.multi_pred_analysis_remove_sequence_to_list, 639 ) 640 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2.clicked.connect( 641 self.multi_pred_analysis_add_protein_to_predict, 642 ) 643 self._view.ui.btn_pred_analysis_multi_back_2.clicked.connect(self.multi_pred_analysis_back_2) 644 645 self._view.ui.txt_pred_analysis_multi_prot_name.textChanged.connect( 646 self.multi_pred_analysis_validate_protein_name, 647 ) 648 self._view.ui.txt_pred_analysis_multi_prot_seq.textChanged.connect( 649 self.multi_pred_analysis_validate_protein_sequence, 650 ) 651 self._view.ui.btn_pred_analysis_multi_advanced_config.clicked.connect(self.show_prediction_configuration) 652 self._view.ui.btn_pred_analysis_multi_go_analysis_setup.clicked.connect(self.switch_multimer_pred_analysis_tab) 653 654 self._view.ui.list_pred_analysis_multi_prot_seq_overview.clicked.connect( 655 self.multi_pred_analysis_prot_seq_overview_item_changed, 656 ) 657 self._view.ui.table_pred_analysis_multi_prot_to_predict.itemSelectionChanged.connect( 658 self.multi_pred_analysis_prot_to_predict_item_changed, 659 ) 660 661 # </editor-fold> 662 663 # <editor-fold desc="Analysis section"> 664 self._view.ui.btn_pred_analysis_multi_add.clicked.connect(self.multi_pred_analysis_structure_analysis_add) 665 self._view.ui.btn_pred_analysis_multi_remove.clicked.connect(self.remove_multi_pred_analysis_analysis_run) 666 self._view.ui.btn_pred_analysis_multi_back_3.clicked.connect(self.multi_pred_analysis_structure_analysis_back_3) 667 self._view.ui.btn_pred_analysis_multi_next_2.clicked.connect(self.multi_pred_analysis_structure_analysis_next_2) 668 self._view.ui.btn_pred_analysis_multi_back_4.clicked.connect(self.multi_pred_analysis_structure_analysis_back_4) 669 self._view.ui.btn_pred_analysis_multi_next_3.clicked.connect(self.multi_pred_analysis_structure_analysis_next_3) 670 self._view.ui.btn_pred_analysis_multi_back_5.clicked.connect(self.multi_pred_analysis_structure_analysis_back_5) 671 self._view.ui.btn_pred_analysis_multi_next_4.clicked.connect(self.multi_pred_analysis_structure_analysis_next_4) 672 self._view.ui.box_pred_analysis_multi_prot_struct_1.currentIndexChanged.connect( 673 self.check_multi_pred_analysis_if_prot_structs_are_filled, 674 ) 675 self._view.ui.box_pred_analysis_multi_prot_struct_2.currentIndexChanged.connect( 676 self.check_multi_pred_analysis_if_prot_structs_are_filled, 677 ) 678 self._view.ui.list_pred_analysis_multi_ref_chains.itemSelectionChanged.connect( 679 self.count_multi_pred_analysis_selected_chains_for_prot_struct_1, 680 ) 681 self._view.ui.list_pred_analysis_multi_model_chains.itemSelectionChanged.connect( 682 self.check_multi_pred_analysis_if_same_no_of_chains_selected, 683 ) 684 self._view.ui.btn_pred_analysis_multi_back_pred_setup.clicked.connect(self.switch_multimer_pred_analysis_tab) 685 self._view.ui.btn_pred_analysis_multi_start.clicked.connect(self.start_multimer_prediction_analysis) 686 self._view.ui.list_pred_analysis_multi_overview.clicked.connect( 687 self.multi_pred_analysis_structure_analysis_overview_clicked, 688 ) 689 # </editor-fold> 690 691 # </editor-fold> 692 693 # <editor-fold desc="Structure analysis page"> 694 self._view.ui.btn_analysis_batch_add.clicked.connect(self.structure_analysis_add) 695 self._view.ui.btn_analysis_batch_remove.clicked.connect(self.remove_analysis_run) 696 self._view.ui.btn_analysis_batch_back.clicked.connect(self.structure_analysis_back) 697 self._view.ui.btn_analysis_batch_next.clicked.connect(self.structure_analysis_next) 698 self._view.ui.btn_analysis_batch_back_2.clicked.connect(self.structure_analysis_back_2) 699 self._view.ui.btn_analysis_batch_next_2.clicked.connect(self.structure_analysis_next_2) 700 self._view.ui.btn_analysis_batch_back_3.clicked.connect(self.structure_analysis_back_3) 701 self._view.ui.btn_analysis_batch_next_3.clicked.connect(self.structure_analysis_next_3) 702 self._view.ui.box_analysis_batch_prot_struct_1.currentIndexChanged.connect( 703 self.check_if_prot_structs_are_filled_batch, 704 ) 705 self._view.ui.box_analysis_batch_prot_struct_2.currentIndexChanged.connect( 706 self.check_if_prot_structs_are_filled_batch, 707 ) 708 self._view.ui.list_analysis_batch_ref_chains.itemSelectionChanged.connect( 709 self.count_batch_selected_chains_for_prot_struct_1, 710 ) 711 self._view.ui.list_analysis_batch_model_chains.itemSelectionChanged.connect( 712 self.check_if_same_no_of_chains_selected_batch, 713 ) 714 self._view.ui.btn_analysis_batch_start.clicked.connect(self.start_process_batch) 715 self._view.ui.list_analysis_batch_overview.clicked.connect(self.structure_analysis_overview_clicked) 716 717 # </editor-fold> 718 719 # <editor-fold desc="Analysis images page"> 720 self._view.ui.btn_add_analysis_images_struct_analysis.clicked.connect( 721 self.add_protein_pair_to_image_creation_queue, 722 ) 723 self._view.ui.list_analysis_images_struct_analysis.doubleClicked.connect( 724 self.add_protein_pair_to_image_creation_queue, 725 ) 726 self._view.ui.list_analysis_images_struct_analysis.clicked.connect(self.analysis_images_enable_add) 727 self._view.ui.btn_remove_analysis_images_creation_struct_analysis.clicked.connect( 728 self.remove_protein_pair_from_image_creation_queue, 729 ) 730 self._view.ui.list_analysis_images_creation_struct_analysis.doubleClicked.connect( 731 self.remove_protein_pair_from_image_creation_queue, 732 ) 733 self._view.ui.list_analysis_images_creation_struct_analysis.clicked.connect(self.analysis_images_enable_remove) 734 self._view.ui.btn_start_automatic_image_creation.clicked.connect(self.start_automatic_image_creation) 735 736 # </editor-fold> 737 738 # <editor-fold desc="Results page"> 739 self._view.ui.cb_results_analysis_options.currentIndexChanged.connect(self.load_results) 740 self._view.ui.btn_color_rmsd.clicked.connect(self.color_protein_pair_by_rmsd) 741 self._view.ui.btn_view_struct_alignment.clicked.connect(self.display_structure_alignment) 742 self._view.ui.btn_view_distance_plot.clicked.connect(self.display_distance_plot) 743 self._view.ui.btn_view_distance_histogram.clicked.connect(self.display_distance_histogram) 744 self._view.ui.btn_view_interesting_region.clicked.connect(self.display_interesting_region) 745 self._view.ui.btn_view_distance_table.clicked.connect(self.display_distance_table) 746 747 # </editor-fold> 748 749 # <editor-fold desc="Manage"> 750 self._view.ui.box_manage_choose_protein.activated.connect(self.choose_manage_open_protein) 751 self._view.ui.box_manage_choose_color.activated.connect(self.choose_manage_color_selected_protein) 752 self._view.ui.box_manage_choose_representation.activated.connect(self.choose_manage_representation) 753 self._view.ui.box_manage_choose_bg_color.activated.connect(self.choose_manage_bg_color) 754 self._view.ui.btn_disulfid_bond_show.clicked.connect(self.show_disulfid_bonds_as_sticks) 755 self._view.ui.btn_disulfid_bond_hide.clicked.connect(self.hide_disulfid_bonds_as_sticks) 756 757 # </editor-fold> 758 759 # <editor-fold desc="Image page"> 760 self._view.ui.btn_update_scene.clicked.connect(self.update_scene) 761 self._view.ui.btn_save_scene.clicked.connect(self.save_scene) 762 self._view.ui.btn_save_image.clicked.connect(self.save_image) 763 self._view.ui.btn_preview_image.clicked.connect(self.preview_image) 764 self._view.ui.box_representation.activated.connect(self.show_representation) 765 self._view.ui.box_bg_color.activated.connect(self.choose_bg_color) 766 self._view.ui.box_renderer.activated.connect(self.choose_renderer) 767 self._view.ui.box_ray_trace_mode.activated.connect(self.choose_ray_trace_mode) 768 self._view.ui.box_ray_texture.activated.connect(self.choose_ray_texture) 769 self._view.ui.cb_transparent_bg.stateChanged.connect(self.decide_transparent_bg) 770 self._view.ui.cb_ray_tracing.stateChanged.connect(self.decide_ray_tracing) 771 772 # </editor-fold> 773 774 # <editor-fold desc="Hotspots page"> 775 self._view.ui.list_hotspots_choose_protein.currentItemChanged.connect(self.open_protein_for_hotspots) 776 self._view.ui.btn_hotspots_resi_show.clicked.connect(self.show_resi_sticks) 777 self._view.ui.btn_hotspots_resi_hide.clicked.connect(self.hide_resi_sticks) 778 self._view.ui.btn_hotspots_resi_zoom.clicked.connect(self.zoom_resi_position) 779 780 # </editor-fold> 781 782 def restore_settings(self) -> None: 783 """Restores the settings.xml file to the default values.""" 784 out = gui_utils.warning_dialog_restore_settings("Are you sure you want to restore all settings?") 785 if out: 786 tools.restore_default_settings(self._application_settings) 787 self._view.status_bar.showMessage("Settings were successfully restored.") 788 logging.info("Settings were successfully restored.") 789 else: 790 self._view.status_bar.showMessage("Settings were not modified.") 791 logging.info("Settings were not modified.") 792 793 def quit_app(self) -> None: 794 """Closes the entire plugin.""" 795 self._view.quit_app() 796 797 @staticmethod 798 def clear_all_log_files() -> None: 799 """Clears all log files generated under .pyssa/logs.""" 800 response = basic_boxes.yes_or_no( 801 "Clear log files", 802 "Are you sure you want to delete all log files?", 803 QtWidgets.QMessageBox.Information, 804 ) 805 if response: 806 try: 807 shutil.rmtree(str(constants.LOG_PATH)) 808 except PermissionError: 809 print("The active log file was not deleted.") 810 if len(os.listdir(str(constants.LOG_PATH))) == 1: 811 basic_boxes.ok("Clear log files", "All log files could be deleted.", QtWidgets.QMessageBox.Information) 812 constants.PYSSA_LOGGER.info("All log files were deleted.") 813 else: 814 basic_boxes.ok("Clear log files", "Not all log files could be deleted.", QtWidgets.QMessageBox.Warning) 815 constants.PYSSA_LOGGER.warning("Not all log files were deleted!") 816 817 # <editor-fold desc="Open extra views"> 818 def open_settings_global(self) -> None: 819 """Opens the dialog for the global settings.""" 820 dialog = dialog_settings_global.DialogSettingsGlobal() 821 dialog.exec_() 822 self._application_settings = self._application_settings.deserialize_settings() 823 globals.g_settings = self._application_settings 824 self._workspace_path = globals.g_settings.workspace_path 825 self._workspace_label = QtWidgets.QLabel(f"Current Workspace: {self._workspace_path}") 826 self._setup_statusbar() 827 828 def open_logs(self) -> None: 829 """Opens a file explorer with all log files and can open a log file in the default application.""" 830 file_dialog = QtWidgets.QFileDialog() 831 log_path = str(constants.LOG_PATH) 832 file_dialog.setDirectory(log_path) 833 file_path, _ = file_dialog.getOpenFileName(self._view, "Select a log file to open", "", "LOG File (*.log)") 834 if file_path: 835 os.startfile(file_path) 836 837 @staticmethod 838 def open_tutorial() -> None: 839 """Opens the official tutorial pdf file.""" 840 tmp_dialog = dialog_tutorial_videos.TutorialVideosDialog() 841 tmp_dialog.exec_() 842 843 @staticmethod 844 def open_documentation() -> None: 845 """Opens the official plugin documentation as PDF.""" 846 os.startfile(constants.DOCS_PATH) 847 848 @staticmethod 849 def open_about() -> None: 850 """Opens the About dialog.""" 851 dialog = dialog_about.DialogAbout() 852 dialog.exec_() 853 854 def open_page_information(self) -> None: 855 """Opens the message box, to display extra information based on the page.""" 856 with open( 857 f"{constants.PAGE_HELP_PATHS_DICT[self._view.ui.lbl_page_title.text()]}", 858 "r", 859 encoding="utf-8", 860 ) as file: 861 html_content = file.read() 862 file.close() 863 tmp_dialog = dialog_help.DialogHelp(html_content) 864 tmp_dialog.exec_() 865 866 @staticmethod 867 def open_release_notes_in_standard_application() -> None: 868 """Opens the release notes in the default app.""" 869 os.startfile(constants.CHANGELOG_HTML_PATH) 870 871 # </editor-fold> 872 873 # def open_change_log(self) -> None: 874 # """Opens change log based on the last run pyssa version. 875 # 876 # Notes: 877 # Change log opens only if the last pyssa version is older than the current one. 878 # """ 879 # last_version = f"v{self.get_version_from_latest_log_file(self.get_filepath_of_latest_log_file())}" 880 # if last_version != constants.VERSION_NUMBER: 881 # self.open_release_notes_in_standard_application() 882 # 883 # def get_version_from_latest_log_file(self, a_filepath: pathlib.Path) -> str: 884 # """Gets the pyssa version of the latest log file. 885 # 886 # Args: 887 # a_filepath: the filepath to the latest log file. 888 # """ 889 # with open(str(a_filepath), "r", encoding="utf-8") as file: 890 # file_content = file.read() 891 # file.close() 892 # # Define the regex pattern to extract the version number 893 # pattern = r"PySSA started with version v(\d+\.\d+\.\d+)" 894 # # Search for the pattern in the text 895 # match = re.search(pattern, file_content) 896 # # Check if a match is found 897 # if match: 898 # version_number = match.group(1) 899 # print("Extracted version number:", version_number) 900 # else: 901 # print("Version number not found in the text.") 902 # version_number = None 903 # return version_number 904 # 905 # def get_filepath_of_latest_log_file(self) -> pathlib.Path: 906 # """Gets the filepath of the latest log file. 907 # 908 # Raises: 909 # FileNotFoundError: If no log files can be found in the log directory. 910 # """ 911 # # Get a list of files in the directory 912 # files = [f for f in os.listdir(constants.LOG_PATH) if os.path.isfile(os.path.join(constants.LOG_PATH, f))] 913 # # Filter files to include only log files (adjust the extension accordingly) 914 # log_files = [f for f in files if f.endswith(".log")] 915 # # Check if there are any log files 916 # if not log_files: 917 # raise FileNotFoundError("No log files found in the directory.") 918 # # Get the full path of each log file 919 # log_files_paths = [os.path.join(constants.LOG_PATH, f) for f in log_files] 920 # # Get the latest log file based on modification time 921 # latest_log_file_index = log_files_paths.index(max(log_files_paths, key=os.path.getmtime)) - 1 922 # return pathlib.Path(log_files_paths[latest_log_file_index]) 923 924 # <editor-fold desc="Logic related methods"> 925 926 # <editor-fold desc="New project page functions"> 927 def create_new_project(self) -> None: 928 """Creates a new project with the content of the new page.""" 929 # <editor-fold desc="Checks"> 930 if self._application_settings.wsl_install == 0: 931 basic_boxes.ok( 932 "Create new project", 933 "Please install local colabfold to create a project!", 934 QtWidgets.QMessageBox.Warning, 935 ) 936 return 937 if self._application_settings.local_colabfold == 0: 938 basic_boxes.ok( 939 "Create new project", 940 "Please install local colabfold to create a project!", 941 QtWidgets.QMessageBox.Warning, 942 ) 943 return 944 945 # </editor-fold> 946 947 self._view.wait_spinner.start() 948 an_add_protein_flag: bool = False 949 if self._view.ui.cb_new_add_reference.checkState() == 2: 950 an_add_protein_flag = True 951 952 self._active_task = tasks.Task( 953 target=main_presenter_async.create_new_project, 954 args=( 955 self._view.ui.txt_new_project_name.text(), 956 self._workspace_path, 957 an_add_protein_flag, 958 self._view.ui.txt_new_choose_reference.text(), 959 ), 960 post_func=self.__await_create_new_project, 961 ) 962 self._active_task.start() 963 self.update_status("Creating new project ...") 964 965 def __await_create_new_project(self, a_result: tuple) -> None: 966 self._current_project: "project.Project" = a_result[1] 967 constants.PYSSA_LOGGER.info(f"Created the project {self._current_project.get_project_name()}.") 968 self._view.ui.cb_new_add_reference.setCheckState(0) 969 self._project_watcher.current_project = self._current_project 970 constants.PYSSA_LOGGER.info( 971 f"{self._project_watcher.current_project.get_project_name()} is the current project.", 972 ) 973 self._project_watcher.on_home_page = False 974 # update gui 975 self._project_watcher.show_valid_options(self._view.ui) 976 self._view.ui.lbl_current_project_name.setText(self._current_project.get_project_name()) 977 self.main_window_state = main_window_state.MainWindowState( 978 results_state.ResultsState(), 979 image_state.ImageState(), 980 ) 981 self.display_view_page() 982 self._view.wait_spinner.stop() 983 self.update_status(self._workspace_status) 984 985 # </editor-fold> 986 987 # <editor-fold desc="Open project page functions"> 988 def open_project(self) -> None: 989 """Initiates the task to open an existing project.""" 990 self._view.wait_spinner.start() 991 self._active_task = tasks.Task( 992 target=main_presenter_async.open_project, 993 args=( 994 self._workspace_path, 995 self._view.ui.txt_open_selected_project.text(), 996 self._application_settings, 997 ), 998 post_func=self.__await_open_project, 999 ) 1000 self._active_task.start() 1001 self.update_status("Opening existing project ...") 1002 1003 def __await_open_project(self, a_result: tuple) -> None: 1004 self._current_project = a_result[1] 1005 self._project_watcher.current_project = self._current_project 1006 constants.PYSSA_LOGGER.info( 1007 f"{self._project_watcher.current_project.get_project_name()} is the current project.", 1008 ) 1009 self._view.ui.lbl_current_project_name.setText(self._current_project.get_project_name()) 1010 self._project_watcher.on_home_page = False 1011 self._project_watcher.show_valid_options(self._view.ui) 1012 cmd.reinitialize() 1013 self._view.ui.btn_manage_session.hide() 1014 self.display_view_page() 1015 self.main_window_state = main_window_state.MainWindowState( 1016 results_state.ResultsState(), 1017 image_state.ImageState(), 1018 ) 1019 self._view.wait_spinner.stop() 1020 self.update_status(self._workspace_status) 1021 1022 # </editor-fold> 1023 1024 # <editor-fold desc="Delete project page functions"> 1025 def delete_project(self) -> None: 1026 """Deletes an existing project.""" 1027 # popup message which warns the user that the selected project gets deleted 1028 response: bool = gui_utils.warning_message_project_gets_deleted() 1029 tmp_project_name = self._view.ui.txt_delete_selected_projects.text() 1030 if response is True: 1031 os.remove(pathlib.Path(f"{self._workspace_path}/{self._view.ui.txt_delete_selected_projects.text()}")) 1032 if self._view.ui.txt_delete_selected_projects.text() == self._view.ui.lbl_current_project_name.text(): 1033 self._view.ui.lbl_current_project_name.clear() 1034 self._view.ui.txt_delete_selected_projects.clear() 1035 # update list 1036 self._view.ui.list_delete_projects.clear() 1037 # pre-process 1038 self._view.status_bar.showMessage(self._workspace_label.text()) 1039 self._view.ui.list_delete_projects.clear() 1040 self._view.status_bar.showMessage(self._workspace_label.text()) 1041 tools.scan_workspace_for_valid_projects(self._workspace_path, self._view.ui.list_delete_projects) 1042 constants.PYSSA_LOGGER.info(f"The project {tmp_project_name} was successfully deleted.") 1043 if self._view.ui.list_delete_projects.count() == 0: 1044 self.display_home_page() 1045 self._project_watcher.check_workspace_for_projects(self._workspace_path, self._view.ui) 1046 else: 1047 constants.PYSSA_LOGGER.info("No project has been deleted. No changes were made.") 1048 1049 # </editor-fold> 1050 1051 # <editor-fold desc="Save project functions"> 1052 def save_project(self) -> None: 1053 """Saves the project.xml.""" 1054 self._view.wait_spinner.start() 1055 self.last_sidebar_button = styles.color_sidebar_buttons( 1056 self.last_sidebar_button, 1057 self._view.ui.btn_save_project, 1058 ) 1059 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 1060 self._active_task = tasks.Task( 1061 target=main_presenter_async.save_project, 1062 args=(self._current_project, 0), 1063 post_func=self.__await_save_project, 1064 ) 1065 self._active_task.start() 1066 self.update_status("Saving current project ...") 1067 1068 def __await_save_project(self, result: tuple) -> None: 1069 self._view.wait_spinner.stop() 1070 self.update_status(self._workspace_status) 1071 basic_boxes.ok("Save Project", "The project was successfully saved.", QtWidgets.QMessageBox.Information) 1072 1073 # </editor-fold> 1074 1075 # <editor-fold desc="Edit project page functions"> 1076 def check_for_cleaning(self) -> None: 1077 """Checks if the selected protein can be cleaned.""" 1078 self._view.wait_spinner.start() 1079 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 1080 try: 1081 tmp_protein_name: str = self._view.ui.list_edit_project_proteins.currentItem().text() 1082 except AttributeError: 1083 self._view.wait_spinner.stop() 1084 return 1085 self._active_task = tasks.Task( 1086 target=main_presenter_async.check_for_cleaning, 1087 args=( 1088 tmp_protein_name, 1089 self._current_project, 1090 ), 1091 post_func=self.__await_check_for_cleaning, 1092 ) 1093 self._active_task.start() 1094 self.update_status("Checking protein properties ...") 1095 1096 def __await_check_for_cleaning(self, result: tuple) -> None: 1097 # check if selected protein contains any organic or solvent molecules which can be removed 1098 tmp_is_cleanable: bool = result[1] 1099 tmp_is_in_protein_pair: bool = result[2] 1100 if tmp_is_cleanable: 1101 gui_elements_to_show = [ 1102 self._view.ui.lbl_edit_clean_new_prot, 1103 self._view.ui.btn_edit_clean_new_prot, 1104 self._view.ui.lbl_edit_clean_update_prot, 1105 self._view.ui.btn_edit_clean_update_prot, 1106 ] 1107 gui_utils.show_gui_elements(gui_elements_to_show) 1108 else: 1109 gui_elements_to_hide = [ 1110 self._view.ui.lbl_edit_clean_new_prot, 1111 self._view.ui.btn_edit_clean_new_prot, 1112 self._view.ui.lbl_edit_clean_update_prot, 1113 self._view.ui.btn_edit_clean_update_prot, 1114 ] 1115 gui_utils.hide_gui_elements(gui_elements_to_hide) 1116 # check if selected protein is in any existing protein pair 1117 if tmp_is_in_protein_pair: 1118 gui_elements_to_hide = [ 1119 self._view.ui.label_12, 1120 self._view.ui.btn_edit_project_delete, 1121 ] 1122 gui_utils.hide_gui_elements(gui_elements_to_hide) 1123 else: 1124 gui_elements_to_show = [ 1125 self._view.ui.label_12, 1126 self._view.ui.btn_edit_project_delete, 1127 ] 1128 gui_utils.show_gui_elements(gui_elements_to_show) 1129 self._view.ui.btn_edit_project_save.show() 1130 self._view.ui.label_13.show() 1131 self._view.ui.label_15.show() 1132 self._view.ui.btn_edit_protein_rename.show() 1133 self._view.ui.btn_manage_session.show() 1134 self._project_watcher.show_valid_options(self._view.ui) 1135 self._view.wait_spinner.stop() 1136 self.update_status(self._workspace_status) 1137 1138 def clean_protein_new(self) -> None: 1139 """Cleans the selected protein structure and creates a new cleaned structure.""" 1140 self._view.wait_spinner.start() 1141 self._active_task = tasks.Task( 1142 target=main_presenter_async.clean_protein_new, 1143 args=( 1144 self._view.ui.list_edit_project_proteins.currentItem().text().replace(".pdb", ""), 1145 self._current_project, 1146 ), 1147 post_func=self.__await_clean_protein_new, 1148 ) 1149 self._active_task.start() 1150 self.update_status("Duplicating and cleaning protein ...") 1151 1152 def __await_clean_protein_new(self, result: tuple) -> None: 1153 self._init_edit_page() 1154 self._project_watcher.show_valid_options(self._view.ui) 1155 self._view.wait_spinner.stop() 1156 self.update_status(self._workspace_status) 1157 1158 def clean_protein_update(self) -> None: 1159 """Cleans the selected protein structure.""" 1160 self._view.wait_spinner.start() 1161 if basic_boxes.yes_or_no( 1162 "Clean protein", 1163 "Are you sure you want to clean this protein?\n" "This will remove all organic and solvent components!", 1164 QtWidgets.QMessageBox.Information, 1165 ): 1166 self._active_task = tasks.Task( 1167 target=main_presenter_async.clean_protein_update, 1168 args=( 1169 self._view.ui.list_edit_project_proteins.currentItem().text().replace(".pdb", ""), 1170 self._current_project, 1171 ), 1172 post_func=self.__await_clean_protein_update, 1173 ) 1174 self._active_task.start() 1175 self.update_status("Cleaning protein ...") 1176 else: 1177 constants.PYSSA_LOGGER.info("No protein has been cleaned.") 1178 self._view.wait_spinner.stop() 1179 1180 def __await_clean_protein_update(self) -> None: 1181 self._init_edit_page() 1182 self._project_watcher.show_valid_options(self._view.ui) 1183 self._view.wait_spinner.stop() 1184 self.update_status(self._workspace_status) 1185 1186 def delete_protein(self) -> None: 1187 """Deletes the selected protein structure.""" 1188 self._view.wait_spinner.start() 1189 if gui_utils.warning_message_protein_gets_deleted(): 1190 self._active_task = tasks.Task( 1191 target=main_presenter_async.delete_protein, 1192 args=( 1193 self._view.ui.list_edit_project_proteins.currentItem().text(), 1194 self._current_project, 1195 ), 1196 post_func=self.__await_delete_protein, 1197 ) 1198 self._active_task.start() 1199 self.update_status("Deleting protein ...") 1200 else: 1201 constants.PYSSA_LOGGER.info("No protein was deleted.") 1202 self._view.wait_spinner.stop() 1203 1204 def __await_delete_protein(self) -> None: 1205 self._init_edit_page() 1206 self._project_watcher.show_valid_options(self._view.ui) 1207 self._view.wait_spinner.stop() 1208 self.update_status(self._workspace_status) 1209 1210 def add_existing_protein(self) -> None: 1211 """Opens a dialog to adds an existing protein structure to the project.""" 1212 self.tmp_dialog = view_add_protein.AddProteinView() 1213 self.tmp_dialog.return_value.connect(self.post_add_existing_protein) 1214 self.tmp_dialog.show() 1215 1216 def post_add_existing_protein(self, return_value: tuple) -> None: 1217 """Adds an existing protein structure to the current project either by id or from the filesystem. 1218 1219 Args: 1220 return_value: a tuple consisting of the filepath or PDB id and the length of the first one. 1221 """ 1222 self._view.wait_spinner.start() 1223 if return_value[1] > 0: 1224 self._active_task = tasks.Task( 1225 target=main_presenter_async.add_existing_protein_to_project, 1226 args=(return_value, self._current_project), 1227 post_func=self.__await_post_add_existing_protein, 1228 ) 1229 self._active_task.start() 1230 self.update_status("Adding protein to current project ...") 1231 else: 1232 self._view.wait_spinner.stop() 1233 self.display_edit_page() 1234 1235 def __await_post_add_existing_protein(self, result: tuple) -> None: 1236 self._current_project = result[1] 1237 self._project_watcher.show_valid_options(self._view.ui) 1238 self._view.wait_spinner.stop() 1239 self.update_status(self._workspace_status) 1240 self.display_edit_page() 1241 1242 def save_selected_protein_structure_as_pdb_file(self) -> None: 1243 """Saves selected protein as pdb file.""" 1244 self._view.wait_spinner.start() 1245 file_dialog = QtWidgets.QFileDialog() 1246 desktop_path = QtCore.QStandardPaths.standardLocations(QtCore.QStandardPaths.DesktopLocation)[0] 1247 file_dialog.setDirectory(desktop_path) 1248 file_path, _ = file_dialog.getSaveFileName( 1249 self._view, 1250 "Save protein structure", 1251 "", 1252 "Protein Data Bank File (*.pdb)", 1253 ) 1254 if file_path: 1255 self._active_task = tasks.Task( 1256 target=main_presenter_async.save_selected_protein_structure_as_pdb_file, 1257 args=(self._view.ui.list_edit_project_proteins.currentItem().text(), self._current_project, file_path), 1258 post_func=self.__await_save_selected_protein_structure_as_pdb_file, 1259 ) 1260 self._active_task.start() 1261 else: 1262 self._view.wait_spinner.stop() 1263 1264 def __await_save_selected_protein_structure_as_pdb_file(self, result: tuple) -> None: 1265 self._view.wait_spinner.stop() 1266 if result[0] == exit_codes.EXIT_CODE_ONE_UNKNOWN_ERROR[0]: 1267 basic_boxes.ok( 1268 "Save protein structure", 1269 "Saving the protein as .pdb file failed!", 1270 QtWidgets.QMessageBox.Error, 1271 ) 1272 elif result[0] == exit_codes.EXIT_CODE_ZERO[0]: 1273 basic_boxes.ok( 1274 "Save protein structure", 1275 "The protein was successfully saved as .pdb file.", 1276 QtWidgets.QMessageBox.Information, 1277 ) 1278 else: 1279 basic_boxes.ok( 1280 "Save protein structure", 1281 "Saving the protein as .pdb file failed with an unexpected error!", 1282 QtWidgets.QMessageBox.Error, 1283 ) 1284 self._project_watcher.show_valid_options(self._view.ui) 1285 self.update_status(self._workspace_status) 1286 1287 def rename_selected_protein_structure(self) -> None: 1288 """Opens a new view to rename the selected protein.""" 1289 self._view.wait_spinner.start() 1290 self.tmp_dialog = dialog_rename_protein.DialogRenameProtein(self._workspace_path) 1291 self.tmp_dialog.return_value.connect(self.post_rename_selected_protein_structure) 1292 self.tmp_dialog.show() 1293 1294 def post_rename_selected_protein_structure(self, return_value: tuple) -> None: 1295 """Renames a selected protein structure.""" 1296 if return_value[1] is True: 1297 self._active_task = tasks.Task( 1298 target=main_presenter_async.rename_selected_protein_structure, 1299 args=( 1300 self._view.ui.list_edit_project_proteins.currentItem().text(), 1301 return_value[0], 1302 self._current_project, 1303 ), 1304 post_func=self.__await_post_rename_selected_protein_structure, 1305 ) 1306 self._active_task.start() 1307 else: 1308 self._view.wait_spinner.stop() 1309 1310 def __await_post_rename_selected_protein_structure(self, result: tuple) -> None: 1311 self._init_edit_page() 1312 self._project_watcher.show_valid_options(self._view.ui) 1313 self._view.wait_spinner.stop() 1314 1315 # </editor-fold> 1316 1317 # <editor-fold desc="View project page functions"> 1318 def view_structure(self) -> None: 1319 """Displays the structure of the selected protein in pymol.""" 1320 protein_name = self._view.ui.list_view_project_proteins.currentItem().text() 1321 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 1322 cmd.reinitialize() 1323 self._view.ui.btn_manage_session.show() 1324 try: 1325 self._current_project.search_protein(protein_name).load_protein_pymol_session() 1326 constants.PYSSA_LOGGER.info("Loaded PyMOL session of protein %s", protein_name) 1327 except pymol.CmdException: 1328 constants.PYSSA_LOGGER.error("Error while loading protein in PyMOL!") 1329 return 1330 self.current_session = current_session.CurrentSession( 1331 "protein", 1332 protein_name, 1333 self._current_project.search_protein(protein_name).pymol_session, 1334 ) 1335 print(self.current_session) 1336 1337 # </editor-fold> 1338 1339 # <editor-fold desc="Use project page functions"> 1340 def display_use_page(self) -> None: 1341 """Displays the use project page.""" 1342 self._view.wait_spinner.start() 1343 if self.is_distance_plot_open: 1344 self.distance_plot_dialog.close() 1345 self.is_distance_plot_open = False 1346 1347 self.start_worker_thread( 1348 task_workers.LoadUsePageWorker( 1349 self._workspace_path, 1350 self._current_project.convert_list_of_proteins_to_list_of_protein_infos(), 1351 ), 1352 self.post_display_use_page, 1353 ) 1354 self._init_use_page() 1355 1356 def post_display_use_page(self, return_value) -> None: # noqa: ANN001 1357 """Displays the use project page, after cpu intense task (post thread method). 1358 1359 Args: 1360 return_value: the value which gets returned from the thread process 1361 """ 1362 # this for-loop is necessary for eliminating all proteins which are in the current project from the ones which 1363 # are available 1364 for tmp_item in return_value[0]: 1365 self._view.ui.list_use_available_protein_structures.addItem(tmp_item) 1366 for i in range(self._view.ui.list_use_selected_protein_structures.count()): 1367 self._view.ui.list_use_selected_protein_structures.setCurrentRow(i) 1368 tmp_prot_name = self._view.ui.list_use_selected_protein_structures.currentItem().text() 1369 if tmp_prot_name in return_value[1]: 1370 return_value[1].remove(tmp_prot_name) 1371 1372 for tmp_item in return_value[1]: 1373 self._view.ui.list_use_available_protein_structures.addItem(tmp_item) 1374 for tmp_project_name in return_value[2]: 1375 self._view.ui.list_use_existing_projects.addItem(QtWidgets.QListWidgetItem(tmp_project_name)) 1376 1377 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 14, "Use existing project") 1378 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_use_page) 1379 self._view.wait_spinner.stop() 1380 1381 def pre_create_use_project(self) -> None: 1382 """Sets up the worker for the create_use_project task.""" 1383 QtWidgets.QApplication.setOverrideCursor(Qt.WaitCursor) 1384 # copy proteins in new project 1385 proteins_to_copy = [] 1386 for i in range(self._view.ui.list_use_selected_protein_structures.count()): 1387 self._view.ui.list_use_selected_protein_structures.setCurrentRow(i) 1388 proteins_to_copy.append(self._view.ui.list_use_selected_protein_structures.currentItem().text()) 1389 1390 # <editor-fold desc="Worker setup"> 1391 # --Begin: worker setup 1392 self.tmp_thread = QtCore.QThread() 1393 self.tmp_worker = task_workers.CreateUseProjectWorker(self._workspace_path, proteins_to_copy) 1394 self.tmp_thread = task_workers.setup_worker_for_work(self.tmp_thread, self.tmp_worker, self.create_use_project) 1395 self.tmp_thread.start() 1396 # --End: worker setup 1397 1398 # </editor-fold> 1399 1400 self._view.ui.lbl_current_project_name.setText(self._view.ui.txt_use_project_name.text()) 1401 self._view.status_bar.showMessage(f"Creating new project: {self._view.ui.txt_use_project_name.text()} ...") 1402 # save project folder in current workspace 1403 new_project = project.Project(self._view.ui.txt_use_project_name.text(), self._workspace_path) 1404 # new_project.create_project_tree() 1405 self._current_project = new_project 1406 1407 def create_use_project(self, proteins_for_new_project) -> None: # noqa: ANN001 1408 """Post thread method. 1409 1410 Args: 1411 proteins_for_new_project (list): the proteins which are in the new project 1412 """ 1413 for tmp_protein_obj in proteins_for_new_project: 1414 self._current_project.add_existing_protein(tmp_protein_obj) 1415 self._current_project.serialize_project( 1416 pathlib.Path(f"{self._workspace_path}/{self._current_project.get_project_name()}.xml"), 1417 ) 1418 # shows options which can be done with the data in the project folder 1419 self._project_watcher.current_project = self._current_project 1420 self._project_watcher.on_home_page = False 1421 self._project_watcher.show_valid_options(self._view.ui) 1422 self.project_scanner.project = self._current_project 1423 self._init_use_page() 1424 constants.PYSSA_LOGGER.info( 1425 f"The project {self._current_project.get_project_name()} was successfully created through a use.", 1426 ) 1427 self.display_view_page() 1428 QtWidgets.QApplication.restoreOverrideCursor() 1429 1430 # </editor-fold> 1431 1432 # <editor-fold desc="Import, Export functions"> 1433 def import_project(self) -> None: 1434 """Imports a project.xml into the current workspace.""" 1435 self.last_sidebar_button = styles.color_sidebar_buttons( 1436 self.last_sidebar_button, 1437 self._view.ui.btn_import_project, 1438 ) 1439 file_dialog = QtWidgets.QFileDialog() 1440 desktop_path = QtCore.QStandardPaths.standardLocations(QtCore.QStandardPaths.DesktopLocation)[0] 1441 file_dialog.setDirectory(desktop_path) 1442 file_path, _ = file_dialog.getOpenFileName( 1443 self._view, 1444 "Select a project file to import", 1445 "", 1446 "XML Files (*.xml)", 1447 ) 1448 if file_path: 1449 tmp_project = project.Project("", self._workspace_path) 1450 tmp_project = tmp_project.deserialize_project(pathlib.Path(file_path), self._application_settings) 1451 tmp_project.set_workspace_path(self._workspace_path) 1452 if len(tmp_project.proteins) <= 1: 1453 if self._application_settings.wsl_install == 0: 1454 basic_boxes.ok( 1455 "Create new project", 1456 "Please install local colabfold to import this project!", 1457 QtWidgets.QMessageBox.Warning, 1458 ) 1459 return 1460 elif self._application_settings.local_colabfold == 0: # noqa: RET505 1461 basic_boxes.ok( 1462 "Create new project", 1463 "Please install local colabfold to import this project!", 1464 QtWidgets.QMessageBox.Warning, 1465 ) 1466 return 1467 new_filepath = pathlib.Path(f"{self._workspace_path}/{tmp_project.get_project_name()}.xml") 1468 tmp_project.serialize_project(new_filepath) 1469 self._current_project = self._current_project.deserialize_project(new_filepath, self._application_settings) 1470 constants.PYSSA_LOGGER.info(f"Opening the project {self._current_project.get_project_name()}.") 1471 self._project_watcher.current_project = self._current_project 1472 self.project_scanner.project = self._current_project 1473 constants.PYSSA_LOGGER.info( 1474 f"{self._project_watcher.current_project.get_project_name()} is the current project.", 1475 ) 1476 self._view.ui.lbl_current_project_name.setText(self._current_project.get_project_name()) 1477 self._project_watcher.on_home_page = False 1478 self._project_watcher.show_valid_options(self._view.ui) 1479 self._view.ui.btn_manage_session.show() 1480 self.display_view_page() 1481 basic_boxes.ok( 1482 "Import Project", 1483 "The project was successfully imported.", 1484 QtWidgets.QMessageBox.Information, 1485 ) 1486 1487 def export_current_project(self) -> None: 1488 """Exports the current project to an importable format.""" 1489 if self.is_distance_plot_open: 1490 self.distance_plot_dialog.close() 1491 self.is_distance_plot_open = False 1492 self.last_sidebar_button = styles.color_sidebar_buttons( 1493 self.last_sidebar_button, 1494 self._view.ui.btn_export_project, 1495 ) 1496 file_dialog = QtWidgets.QFileDialog() 1497 desktop_path = QtCore.QStandardPaths.standardLocations(QtCore.QStandardPaths.DesktopLocation)[0] 1498 file_dialog.setDirectory(desktop_path) 1499 file_path, _ = file_dialog.getSaveFileName(self._view, "Save current project", "", "XML Files (*.xml)") 1500 if file_path: 1501 self._current_project.serialize_project(pathlib.Path(file_path)) 1502 basic_boxes.ok( 1503 "Export Project", 1504 "The project was successfully exported.", 1505 QtWidgets.QMessageBox.Information, 1506 ) 1507 1508 # </editor-fold> 1509 1510 # <editor-fold desc="Close project functions"> 1511 def close_project(self) -> None: 1512 """Closes the current project.""" 1513 if self.is_distance_plot_open: 1514 self.distance_plot_dialog.close() 1515 self.is_distance_plot_open = False 1516 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 1517 cmd.reinitialize() 1518 self._view.ui.list_hotspots_choose_protein.clear() 1519 self._project_watcher.on_home_page = True 1520 self._project_watcher.current_project = project.Project("", pathlib.Path("")) 1521 self._project_watcher.show_valid_options(self._view.ui) 1522 self._view.ui.lbl_current_project_name.setText("") 1523 self._init_all_pages() 1524 self.results_name = "" 1525 constants.PYSSA_LOGGER.info(f"The project {self._current_project.get_project_name()} was closed") 1526 self.display_home_page() 1527 1528 # </editor-fold> 1529 1530 # <editor-fold desc="ESMFold Monomer functions"> 1531 def post_predict_esm_monomer(self, output) -> None: # noqa: ANN001 1532 """Post thread method, for the prediction process. 1533 1534 Args: 1535 output (list): the proteins which got predicted 1536 """ 1537 self.block_box_prediction.destroy(True) 1538 for tmp_filename in os.listdir(constants.ESMFOLD_PDB_DIR): 1539 constants.PYSSA_LOGGER.info( 1540 f"Add protein {tmp_filename} to the current project {self._current_project.get_project_name()}", 1541 ) 1542 self._current_project.add_existing_protein( 1543 protein.Protein( 1544 tmp_filename.replace(".pdb", ""), 1545 path_util.FilePath(pathlib.Path(f"{constants.ESMFOLD_PDB_DIR}/{tmp_filename}")), 1546 ), 1547 ) 1548 if len(output) > 0: 1549 formatted_output = ", ".join(output) 1550 basic_boxes.ok( 1551 "ESMFold Prediction", 1552 f"These protein prediction failed: {formatted_output}.", 1553 QtWidgets.QMessageBox.Critical, 1554 ) 1555 else: 1556 basic_boxes.ok("ESMFold Prediction", "The prediction was successful.", QtWidgets.QMessageBox.Information) 1557 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 1558 self.display_view_page() 1559 self._project_watcher.show_valid_options(self._view.ui) 1560 1561 def predict_esm_monomer(self) -> None: 1562 """Sets up the worker to predict the proteins with the ESM-Fold.""" 1563 # <editor-fold desc="Worker setup"> 1564 # --Begin: worker setup 1565 self.tmp_thread = QtCore.QThread() 1566 self.tmp_worker = task_workers.EsmFoldWorker(self._view.ui.table_esm_prot_to_predict) 1567 self.tmp_thread = task_workers.setup_worker_for_work( 1568 self.tmp_thread, 1569 self.tmp_worker, 1570 self.post_predict_esm_monomer, 1571 ) 1572 self.tmp_thread.start() 1573 # --End: worker setup 1574 1575 # </editor-fold> 1576 1577 self.block_box_prediction = QtWidgets.QMessageBox() 1578 self.block_box_prediction = gui_utils.setup_standard_block_box( 1579 self.block_box_prediction, 1580 "Structure Prediction", 1581 "A prediction is currently running.", 1582 ) 1583 # self.block_box_prediction.setStandardButtons(QtWidgets.QMessageBox.NoButton) 1584 # self.block_box_prediction.setIcon(QtWidgets.QMessageBox.Information) 1585 # self.block_box_prediction.setWindowIcon( 1586 # PyQt5.constants.PLUGIN_LOGO_ICON_OBJ) 1587 # styles.set_stylesheet(self.block_box_prediction) 1588 # self.block_box_prediction.setWindowTitle("Structure Prediction") 1589 # self.block_box_prediction.setText("A prediction is currently running.") 1590 self.block_box_prediction.exec_() 1591 1592 # </editor-fold> 1593 1594 # <editor-fold desc="Monomer Local Prediction functions"> 1595 def post_prediction_process(self, an_exit_code: int, an_exit_code_description: str) -> None: 1596 """Process which runs after each prediction job.""" 1597 if an_exit_code == exit_codes.ERROR_WRITING_FASTA_FILES[0]: 1598 self.block_box_prediction.destroy(True) 1599 basic_boxes.ok( 1600 "Prediction", 1601 "Prediction failed because there was an error writing the fasta file(s)!", 1602 QtWidgets.QMessageBox.Critical, 1603 ) 1604 self.display_view_page() 1605 self._project_watcher.show_valid_options(self._view.ui) 1606 constants.PYSSA_LOGGER.error(f"Prediction ended with exit code {an_exit_code}: {an_exit_code_description}") 1607 elif an_exit_code == exit_codes.ERROR_FASTA_FILES_NOT_FOUND[0]: 1608 self.block_box_prediction.destroy(True) 1609 basic_boxes.ok( 1610 "Prediction", 1611 "Prediction failed because the fasta file(s) could not be found!", 1612 QtWidgets.QMessageBox.Critical, 1613 ) 1614 self.display_view_page() 1615 self._project_watcher.show_valid_options(self._view.ui) 1616 constants.PYSSA_LOGGER.error(f"Prediction ended with exit code {an_exit_code}: {an_exit_code_description}") 1617 elif an_exit_code == exit_codes.ERROR_PREDICTION_FAILED[0]: 1618 self.block_box_prediction.destroy(True) 1619 basic_boxes.ok( 1620 "Prediction", 1621 "Prediction failed because a subprocess failed!", 1622 QtWidgets.QMessageBox.Critical, 1623 ) 1624 self.display_view_page() 1625 self._project_watcher.show_valid_options(self._view.ui) 1626 constants.PYSSA_LOGGER.error(f"Prediction ended with exit code {an_exit_code}: {an_exit_code_description}") 1627 elif an_exit_code == exit_codes.EXIT_CODE_ONE_UNKNOWN_ERROR[0]: 1628 self.block_box_prediction.destroy(True) 1629 basic_boxes.ok( 1630 "Prediction", 1631 "Prediction failed because of an unknown error!", 1632 QtWidgets.QMessageBox.Critical, 1633 ) 1634 self.display_view_page() 1635 self._project_watcher.show_valid_options(self._view.ui) 1636 constants.PYSSA_LOGGER.error(f"Prediction ended with exit code {an_exit_code}: {an_exit_code_description}") 1637 elif an_exit_code == exit_codes.EXIT_CODE_ZERO[0]: 1638 # Prediction was successful 1639 if self.prediction_type == constants.PREDICTION_TYPE_PRED: 1640 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 1641 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 1642 self.block_box_prediction.destroy(True) 1643 basic_boxes.ok( 1644 "Structure prediction", 1645 "All structure predictions are done. Go to View to check the new proteins.", 1646 QtWidgets.QMessageBox.Information, 1647 ) 1648 constants.PYSSA_LOGGER.info("All structure predictions are done.") 1649 self._project_watcher.show_valid_options(self._view.ui) 1650 self._init_local_pred_mono_page() 1651 self._init_local_pred_multi_page() 1652 self.display_view_page() 1653 elif self.prediction_type == constants.PREDICTION_TYPE_PRED_MONO_ANALYSIS: 1654 # executes if monomers were successfully predicted 1655 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 1656 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 1657 constants.PYSSA_LOGGER.info("All structure predictions are done.") 1658 constants.PYSSA_LOGGER.info("Begin analysis process.") 1659 constants.PYSSA_LOGGER.debug( 1660 f"Thread count before analysis worker: {self.threadpool.activeThreadCount()}", 1661 ) 1662 1663 # self.worker_analysis = workers.AnalysisWorkerPool( 1664 # self._view.ui.list_pred_analysis_mono_overview, self._view.ui.cb_pred_analysis_mono_images, 1665 # self._view.status_bar, self._current_project, self._application_settings, self._init_mono_pred_analysis_page) 1666 constants.PYSSA_LOGGER.info("Thread started for analysis process.") 1667 # self.threadpool.start(self.worker_analysis) 1668 constants.PYSSA_LOGGER.debug( 1669 f"Thread count after analysis worker: {self.threadpool.activeThreadCount()}", 1670 ) 1671 1672 # <editor-fold desc="Worker setup"> 1673 # TODO: test code below 1674 # --Begin: worker setup 1675 self.tmp_thread = QtCore.QThread() 1676 self.tmp_worker = task_workers.DistanceAnalysisWorker( 1677 self._view.ui.list_pred_analysis_mono_overview, 1678 self._view.ui.cb_pred_analysis_mono_images, 1679 self._view.status_bar, 1680 self._current_project, 1681 self._application_settings, 1682 self._init_mono_pred_analysis_page, 1683 ) 1684 self.tmp_thread = task_workers.setup_worker_for_work( 1685 self.tmp_thread, 1686 self.tmp_worker, 1687 self.display_view_page, 1688 ) 1689 self.tmp_worker.finished.connect(self.post_analysis_process) 1690 self.tmp_thread.start() 1691 # --End: worker setup 1692 1693 # </editor-fold> 1694 1695 if not os.path.exists(constants.SCRATCH_DIR_ANALYSIS): 1696 os.mkdir(constants.SCRATCH_DIR_ANALYSIS) 1697 self.block_box_prediction.destroy(True) 1698 self.block_box_analysis.exec_() 1699 self.display_view_page() 1700 self._project_watcher.show_valid_options(self._view.ui) 1701 elif self.prediction_type == constants.PREDICTION_TYPE_PRED_MULTI_ANALYSIS: 1702 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 1703 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 1704 constants.PYSSA_LOGGER.info("All structure predictions are done.") 1705 constants.PYSSA_LOGGER.info("Begin analysis process.") 1706 constants.PYSSA_LOGGER.debug( 1707 f"Thread count before analysis worker: {self.threadpool.activeThreadCount()}", 1708 ) 1709 1710 # self.worker_analysis = workers.AnalysisWorkerPool( 1711 # self._view.ui.list_pred_analysis_multi_overview, self._view.ui.cb_pred_analysis_multi_images, 1712 # self._view.status_bar, self._current_project, self._application_settings, self._init_multi_pred_analysis_page) 1713 constants.PYSSA_LOGGER.info("Thread started for analysis process.") 1714 # self.threadpool.start(self.worker_analysis) 1715 constants.PYSSA_LOGGER.debug( 1716 f"Thread count after analysis worker: {self.threadpool.activeThreadCount()}", 1717 ) 1718 1719 # <editor-fold desc="Worker setup"> 1720 # TODO: test code below 1721 # --Begin: worker setup 1722 self.tmp_thread = QtCore.QThread() 1723 self.tmp_worker = task_workers.DistanceAnalysisWorker( 1724 self._view.ui.list_pred_analysis_multi_overview, 1725 self._view.ui.cb_pred_analysis_multi_images, 1726 self._view.status_bar, 1727 self._current_project, 1728 self._application_settings, 1729 self._init_multi_pred_analysis_page, 1730 ) 1731 self.tmp_thread = task_workers.setup_worker_for_work( 1732 self.tmp_thread, 1733 self.tmp_worker, 1734 self.display_view_page, 1735 ) 1736 self.tmp_worker.finished.connect(self.post_analysis_process) 1737 self.tmp_thread.start() 1738 # --End: worker setup 1739 1740 # </editor-fold> 1741 1742 if not os.path.exists(constants.SCRATCH_DIR_ANALYSIS): 1743 os.mkdir(constants.SCRATCH_DIR_ANALYSIS) 1744 self.block_box_prediction.destroy(True) 1745 self.block_box_analysis.exec_() 1746 self.display_view_page() 1747 self._project_watcher.show_valid_options(self._view.ui) 1748 try: 1749 shutil.rmtree(pathlib.Path(f"{constants.SCRATCH_DIR}/local_predictions")) 1750 except Exception as e: 1751 constants.PYSSA_LOGGER.warning(f"Local predictions scratch path could not be deleted. {e}") 1752 1753 def predict_local_monomer(self) -> None: 1754 """Sets tup the worker for the prediction with the colabfold.""" 1755 self._view.wait_spinner.start() 1756 self.prediction_type = constants.PREDICTION_TYPE_PRED 1757 constants.PYSSA_LOGGER.info("Begin prediction process.") 1758 self.update_status("Begin prediction process ...") 1759 predictions: list[ 1760 prediction_protein_info.PredictionProteinInfo 1761 ] = prediction_util.get_prediction_name_and_seq_from_table(self._view.ui.table_pred_mono_prot_to_predict) 1762 1763 self._active_task = tasks.Task( 1764 target=main_presenter_async.predict_protein_with_colabfold, 1765 args=( 1766 predictions, 1767 self.prediction_configuration, 1768 self._current_project, 1769 ), 1770 post_func=self.__await_predict_protein_with_colabfold, 1771 ) 1772 self._active_task.start() 1773 1774 self.block_box_prediction = QtWidgets.QMessageBox() 1775 self.block_box_prediction.setIcon(QtWidgets.QMessageBox.Information) 1776 self.block_box_prediction.setWindowIcon(QtGui.QIcon(constants.PLUGIN_LOGO_FILEPATH)) 1777 styles.set_stylesheet(self.block_box_prediction) 1778 self.block_box_prediction.setWindowTitle("Structure Prediction") 1779 self.block_box_prediction.setText("A prediction is currently running.") 1780 btn_abort = self.block_box_prediction.addButton("Abort", QtWidgets.QMessageBox.ActionRole) 1781 self.block_box_prediction.exec_() 1782 if self.block_box_prediction.clickedButton() == btn_abort: 1783 self.abort_prediction() 1784 self.block_box_prediction.close() 1785 self._view.wait_spinner.stop() 1786 return 1787 else: # noqa: RET505 1788 self.block_box_prediction.close() 1789 self._view.wait_spinner.stop() 1790 1791 def __await_predict_protein_with_colabfold(self, result: tuple) -> None: 1792 """Process which runs after each prediction job.""" 1793 tmp_exit_code = result[0] 1794 tmp_exit_code_description = [1] 1795 if tmp_exit_code == exit_codes.ERROR_WRITING_FASTA_FILES[0]: 1796 self.block_box_prediction.destroy(True) 1797 basic_boxes.ok( 1798 "Prediction", 1799 "Prediction failed because there was an error writing the fasta file(s)!", 1800 QtWidgets.QMessageBox.Critical, 1801 ) 1802 self.display_view_page() 1803 self._project_watcher.show_valid_options(self._view.ui) 1804 constants.PYSSA_LOGGER.error( 1805 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 1806 ) 1807 elif tmp_exit_code == exit_codes.ERROR_FASTA_FILES_NOT_FOUND[0]: 1808 self.block_box_prediction.destroy(True) 1809 basic_boxes.ok( 1810 "Prediction", 1811 "Prediction failed because the fasta file(s) could not be found!", 1812 QtWidgets.QMessageBox.Critical, 1813 ) 1814 self.display_view_page() 1815 self._project_watcher.show_valid_options(self._view.ui) 1816 constants.PYSSA_LOGGER.error( 1817 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 1818 ) 1819 elif tmp_exit_code == exit_codes.ERROR_PREDICTION_FAILED[0]: 1820 self.block_box_prediction.destroy(True) 1821 basic_boxes.ok( 1822 "Prediction", 1823 "Prediction failed because a subprocess failed!", 1824 QtWidgets.QMessageBox.Critical, 1825 ) 1826 self.display_view_page() 1827 self._project_watcher.show_valid_options(self._view.ui) 1828 constants.PYSSA_LOGGER.error( 1829 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 1830 ) 1831 elif tmp_exit_code == exit_codes.EXIT_CODE_ONE_UNKNOWN_ERROR[0]: 1832 self.block_box_prediction.destroy(True) 1833 basic_boxes.ok( 1834 "Prediction", 1835 "Prediction failed because of an unknown error!", 1836 QtWidgets.QMessageBox.Critical, 1837 ) 1838 self.display_view_page() 1839 self._project_watcher.show_valid_options(self._view.ui) 1840 constants.PYSSA_LOGGER.error( 1841 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 1842 ) 1843 elif tmp_exit_code == exit_codes.EXIT_CODE_ZERO[0]: 1844 # Prediction was successful 1845 if self.prediction_type == constants.PREDICTION_TYPE_PRED: 1846 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 1847 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 1848 self.block_box_prediction.destroy(True) 1849 basic_boxes.ok( 1850 "Structure prediction", 1851 "All structure predictions are done. Go to View to check the new proteins.", 1852 QtWidgets.QMessageBox.Information, 1853 ) 1854 constants.PYSSA_LOGGER.info("All structure predictions are done.") 1855 self._project_watcher.show_valid_options(self._view.ui) 1856 self._init_local_pred_mono_page() 1857 self._init_local_pred_multi_page() 1858 self.display_view_page() 1859 self._view.wait_spinner.stop() 1860 1861 def abort_prediction(self) -> None: 1862 """Aborts the running prediction.""" 1863 constants.PYSSA_LOGGER.info("Structure prediction process was aborted manually.") 1864 subprocess.run(["wsl", "--shutdown"]) 1865 constants.PYSSA_LOGGER.info("Shutdown of wsl environment.") 1866 filesystem_io.FilesystemCleaner.clean_prediction_scratch_folder() 1867 constants.PYSSA_LOGGER.info("Cleaned scratch directory.") 1868 basic_boxes.ok("Abort prediction", "The structure prediction was aborted.", QtWidgets.QMessageBox.Information) 1869 self.last_sidebar_button = styles.color_sidebar_buttons( 1870 self.last_sidebar_button, 1871 self._view.ui.btn_prediction_abort, 1872 ) 1873 self._project_watcher.show_valid_options(self._view.ui) 1874 1875 # </editor-fold> 1876 1877 # <editor-fold desc="Multimer Local Prediction functions"> 1878 def predict_local_multimer(self) -> None: 1879 """Sets up the worker for the prediction with the colabfold.""" 1880 self._view.wait_spinner.start() 1881 self.prediction_type = constants.PREDICTION_TYPE_PRED 1882 constants.PYSSA_LOGGER.info("Begin multimer prediction process.") 1883 self.update_status("Begin prediction process ...") 1884 predictions: list[ 1885 prediction_protein_info.PredictionProteinInfo 1886 ] = prediction_util.get_prediction_name_and_seq_from_table(self._view.ui.table_pred_multi_prot_to_predict) 1887 1888 self._active_task = tasks.Task( 1889 target=main_presenter_async.predict_protein_with_colabfold, 1890 args=( 1891 predictions, 1892 self.prediction_configuration, 1893 self._current_project, 1894 ), 1895 post_func=self.__await_predict_protein_with_colabfold, 1896 ) 1897 self._active_task.start() 1898 1899 self.block_box_prediction = QtWidgets.QMessageBox() 1900 self.block_box_prediction.setIcon(QtWidgets.QMessageBox.Information) 1901 self.block_box_prediction.setWindowIcon(QtGui.QIcon(constants.PLUGIN_LOGO_FILEPATH)) 1902 styles.set_stylesheet(self.block_box_prediction) 1903 self.block_box_prediction.setWindowTitle("Structure Prediction") 1904 self.block_box_prediction.setText("A prediction is currently running.") 1905 btn_abort = self.block_box_prediction.addButton("Abort", QtWidgets.QMessageBox.ActionRole) 1906 self.block_box_prediction.exec_() 1907 if self.block_box_prediction.clickedButton() == btn_abort: 1908 self.abort_prediction() 1909 self.block_box_prediction.close() 1910 self._view.wait_spinner.stop() 1911 else: 1912 self.block_box_prediction.close() 1913 self._view.wait_spinner.stop() 1914 1915 # </editor-fold> 1916 1917 # <editor-fold desc="Monomer Prediction + Analysis functions"> 1918 def start_monomer_prediction_analysis(self) -> None: 1919 """Sets up the worker for the prediction of the proteins.""" 1920 self._view.wait_spinner.start() 1921 self.prediction_type = constants.PREDICTION_TYPE_PRED_MONO_ANALYSIS 1922 constants.PYSSA_LOGGER.info("Begin prediction process.") 1923 self.update_status("Begin prediction process ...") 1924 predictions: list[ 1925 prediction_protein_info.PredictionProteinInfo 1926 ] = prediction_util.get_prediction_name_and_seq_from_table( 1927 self._view.ui.table_pred_analysis_mono_prot_to_predict, 1928 ) 1929 1930 self._active_task = tasks.Task( 1931 target=main_presenter_async.predict_protein_with_colabfold, 1932 args=( 1933 predictions, 1934 self.prediction_configuration, 1935 self._current_project, 1936 ), 1937 post_func=self.__await_monomer_prediction_for_subsequent_analysis, 1938 ) 1939 self._active_task.start() 1940 1941 self.block_box_prediction = QtWidgets.QMessageBox() 1942 self.block_box_prediction.setIcon(QtWidgets.QMessageBox.Information) 1943 self.block_box_prediction.setWindowIcon(QtGui.QIcon(constants.PLUGIN_LOGO_FILEPATH)) 1944 styles.set_stylesheet(self.block_box_prediction) 1945 self.block_box_prediction.setWindowTitle("Structure Prediction") 1946 self.block_box_prediction.setText("A prediction is currently running.") 1947 btn_abort = self.block_box_prediction.addButton("Abort", QtWidgets.QMessageBox.ActionRole) 1948 self.block_box_prediction.exec_() 1949 if self.block_box_prediction.clickedButton() == btn_abort: 1950 self.abort_prediction() 1951 self.block_box_prediction.close() 1952 self._view.wait_spinner.stop() 1953 else: 1954 self.block_box_prediction.close() 1955 self._view.wait_spinner.stop() 1956 1957 def __await_monomer_prediction_for_subsequent_analysis(self, result: tuple) -> None: 1958 tmp_exit_code = result[0] 1959 tmp_exit_code_description = [1] 1960 if tmp_exit_code == exit_codes.EXIT_CODE_ZERO[0]: 1961 # Prediction was successful 1962 self.block_box_prediction.destroy(True) 1963 constants.PYSSA_LOGGER.info("All structure predictions are done.") 1964 self.update_status("All structure predictions are done.") 1965 constants.PYSSA_LOGGER.info("Begin analysis process.") 1966 self.update_status("Begin analysis process ...") 1967 1968 tmp_raw_analysis_run_names: list = [] 1969 for row_no in range(self._view.ui.list_pred_analysis_mono_overview.count()): 1970 tmp_raw_analysis_run_names.append(self._view.ui.list_pred_analysis_mono_overview.item(row_no).text()) 1971 1972 self._active_task = tasks.Task( 1973 target=main_presenter_async.run_distance_analysis, 1974 args=( 1975 tmp_raw_analysis_run_names, 1976 self._current_project, 1977 self._application_settings, 1978 self._view.ui.cb_pred_analysis_mono_images.isChecked(), 1979 ), 1980 post_func=self.post_analysis_process, 1981 ) 1982 self._active_task.start() 1983 1984 if not os.path.exists(constants.SCRATCH_DIR_ANALYSIS): 1985 os.mkdir(constants.SCRATCH_DIR_ANALYSIS) 1986 self.block_box_analysis.exec_() 1987 self.display_view_page() 1988 1989 elif tmp_exit_code == exit_codes.ERROR_WRITING_FASTA_FILES[0]: 1990 self.block_box_prediction.destroy(True) 1991 basic_boxes.ok( 1992 "Prediction", 1993 "Prediction failed because there was an error writing the fasta file(s)!", 1994 QtWidgets.QMessageBox.Critical, 1995 ) 1996 self.display_view_page() 1997 self._project_watcher.show_valid_options(self._view.ui) 1998 constants.PYSSA_LOGGER.error( 1999 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 2000 ) 2001 self._view.wait_spinner.stop() 2002 elif tmp_exit_code == exit_codes.ERROR_FASTA_FILES_NOT_FOUND[0]: 2003 self.block_box_prediction.destroy(True) 2004 basic_boxes.ok( 2005 "Prediction", 2006 "Prediction failed because the fasta file(s) could not be found!", 2007 QtWidgets.QMessageBox.Critical, 2008 ) 2009 self.display_view_page() 2010 self._project_watcher.show_valid_options(self._view.ui) 2011 constants.PYSSA_LOGGER.error( 2012 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 2013 ) 2014 self._view.wait_spinner.stop() 2015 elif tmp_exit_code == exit_codes.ERROR_PREDICTION_FAILED[0]: 2016 self.block_box_prediction.destroy(True) 2017 basic_boxes.ok( 2018 "Prediction", 2019 "Prediction failed because a subprocess failed!", 2020 QtWidgets.QMessageBox.Critical, 2021 ) 2022 self.display_view_page() 2023 self._project_watcher.show_valid_options(self._view.ui) 2024 constants.PYSSA_LOGGER.error( 2025 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 2026 ) 2027 self._view.wait_spinner.stop() 2028 elif tmp_exit_code == exit_codes.EXIT_CODE_ONE_UNKNOWN_ERROR[0]: 2029 self.block_box_prediction.destroy(True) 2030 basic_boxes.ok( 2031 "Prediction", 2032 "Prediction failed because of an unknown error!", 2033 QtWidgets.QMessageBox.Critical, 2034 ) 2035 self.display_view_page() 2036 self._project_watcher.show_valid_options(self._view.ui) 2037 constants.PYSSA_LOGGER.error( 2038 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 2039 ) 2040 self._view.wait_spinner.stop() 2041 2042 def mono_pred_analysis_structure_analysis_next_2(self) -> None: 2043 """Shows the gui elements for the chain selection of protein 1.""" 2044 self._view.wait_spinner.start() 2045 tmp_proteins_to_predict: list[str] = [] 2046 for i in range(self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount()): 2047 tmp_proteins_to_predict.append( 2048 self._view.ui.table_pred_analysis_mono_prot_to_predict.verticalHeaderItem(i).text(), 2049 ) 2050 self._active_task = tasks.Task( 2051 target=main_presenter_async.check_chains_for_subsequent_analysis, 2052 args=( 2053 self._view.ui.box_pred_analysis_mono_prot_struct_1.currentText(), 2054 self._view.ui.box_pred_analysis_mono_prot_struct_2.currentText(), 2055 self._current_project, 2056 tmp_proteins_to_predict, 2057 ), 2058 post_func=self.__await_mono_pred_analysis_structure_analysis_next_2, 2059 ) 2060 self._active_task.start() 2061 2062 def __await_mono_pred_analysis_structure_analysis_next_2(self, result: tuple) -> None: 2063 _, tmp_analysis_name = result 2064 if tmp_analysis_name != "": 2065 gui_elements_to_show = [ 2066 self._view.ui.btn_pred_analysis_mono_remove, 2067 self._view.ui.btn_pred_analysis_mono_add, 2068 self._view.ui.lbl_pred_analysis_mono_overview, 2069 self._view.ui.list_pred_analysis_mono_overview, 2070 self._view.ui.lbl_pred_analysis_mono_images, 2071 self._view.ui.cb_pred_analysis_mono_images, 2072 self._view.ui.btn_pred_analysis_mono_start, 2073 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 2074 ] 2075 gui_elements_to_hide = [ 2076 self._view.ui.box_pred_analysis_mono_prot_struct_1, 2077 self._view.ui.box_pred_analysis_mono_prot_struct_2, 2078 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 2079 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 2080 self._view.ui.lbl_analysis_batch_vs_2, 2081 self._view.ui.lbl_pred_analysis_mono_ref_chains, 2082 self._view.ui.list_pred_analysis_mono_ref_chains, 2083 self._view.ui.lbl_pred_analysis_mono_model_chains, 2084 self._view.ui.list_pred_analysis_mono_model_chains, 2085 self._view.ui.btn_pred_analysis_mono_back_3, 2086 self._view.ui.btn_pred_analysis_mono_next_2, 2087 self._view.ui.btn_pred_analysis_mono_back_4, 2088 self._view.ui.btn_pred_analysis_mono_next_3, 2089 self._view.ui.btn_pred_analysis_mono_back_5, 2090 self._view.ui.btn_pred_analysis_mono_next_4, 2091 ] 2092 gui_utils.show_gui_elements(gui_elements_to_show) 2093 gui_utils.hide_gui_elements(gui_elements_to_hide) 2094 item = QtWidgets.QListWidgetItem(tmp_analysis_name) 2095 self._view.ui.list_pred_analysis_mono_overview.addItem(item) 2096 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(False) 2097 else: 2098 gui_elements_to_show = [ 2099 self._view.ui.lbl_pred_analysis_mono_overview, 2100 self._view.ui.list_pred_analysis_mono_overview, 2101 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 2102 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 2103 self._view.ui.lbl_analysis_batch_vs_2, 2104 self._view.ui.lbl_pred_analysis_mono_ref_chains, 2105 self._view.ui.list_pred_analysis_mono_ref_chains, 2106 self._view.ui.btn_pred_analysis_mono_back_4, 2107 self._view.ui.btn_pred_analysis_mono_next_3, 2108 ] 2109 gui_elements_to_hide = [ 2110 self._view.ui.btn_pred_analysis_mono_remove, 2111 self._view.ui.btn_pred_analysis_mono_add, 2112 self._view.ui.box_pred_analysis_mono_prot_struct_1, 2113 self._view.ui.box_pred_analysis_mono_prot_struct_2, 2114 self._view.ui.btn_pred_analysis_mono_back_3, 2115 self._view.ui.btn_pred_analysis_mono_next_2, 2116 self._view.ui.lbl_pred_analysis_mono_model_chains, 2117 self._view.ui.list_pred_analysis_mono_model_chains, 2118 self._view.ui.btn_pred_analysis_mono_back_5, 2119 self._view.ui.btn_pred_analysis_mono_next_4, 2120 self._view.ui.lbl_pred_analysis_mono_images, 2121 self._view.ui.cb_pred_analysis_mono_images, 2122 self._view.ui.btn_pred_analysis_mono_start, 2123 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 2124 ] 2125 gui_utils.show_gui_elements(gui_elements_to_show) 2126 gui_utils.hide_gui_elements(gui_elements_to_hide) 2127 self._view.ui.lbl_pred_analysis_mono_prot_struct_1.setText( 2128 self._view.ui.box_pred_analysis_mono_prot_struct_1.currentText(), 2129 ) 2130 self._view.ui.lbl_pred_analysis_mono_prot_struct_2.setText( 2131 self._view.ui.box_pred_analysis_mono_prot_struct_2.currentText(), 2132 ) 2133 self._view.ui.list_pred_analysis_mono_ref_chains.clear() 2134 self._view.ui.btn_pred_analysis_mono_next_3.setEnabled(False) 2135 self._view.ui.list_pred_analysis_mono_ref_chains.setEnabled(True) 2136 2137 for i in range(self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount()): 2138 if ( 2139 self._view.ui.table_pred_analysis_mono_prot_to_predict.verticalHeaderItem(i).text() 2140 == self._view.ui.box_pred_analysis_mono_prot_struct_1.currentText() 2141 ): 2142 self._view.ui.list_pred_analysis_mono_ref_chains.addItem( 2143 self._view.ui.table_pred_analysis_mono_prot_to_predict.item(i, 0).text(), 2144 ) 2145 if self._view.ui.list_pred_analysis_mono_ref_chains.count() == 0: 2146 tmp_protein = self._current_project.search_protein( 2147 self._view.ui.box_pred_analysis_mono_prot_struct_1.currentText(), 2148 ) 2149 for tmp_chain in tmp_protein.chains: 2150 if tmp_chain.chain_type == "protein_chain": 2151 self._view.ui.list_pred_analysis_mono_ref_chains.addItem(tmp_chain.chain_letter) 2152 if self._view.ui.list_pred_analysis_mono_ref_chains.count() == 1: 2153 self._view.ui.lbl_pred_analysis_mono_ref_chains.setText( 2154 f"Select chain in protein structure {self._view.ui.lbl_pred_analysis_mono_prot_struct_1.text()}.", 2155 ) 2156 else: 2157 self._view.ui.lbl_pred_analysis_mono_ref_chains.setText( 2158 f"Select chains in protein structure {self._view.ui.lbl_pred_analysis_mono_prot_struct_1.text()}.", 2159 ) 2160 self._view.wait_spinner.stop() 2161 2162 # </editor-fold> 2163 2164 # <editor-fold desc="Multimer Prediction + Analysis functions"> 2165 def start_multimer_prediction_analysis(self) -> None: 2166 """Sets up the prediction process.""" 2167 self._view.wait_spinner.start() 2168 self.prediction_type = constants.PREDICTION_TYPE_PRED_MULTI_ANALYSIS 2169 constants.PYSSA_LOGGER.info("Begin prediction process.") 2170 self.update_status("Begin prediction process ...") 2171 predictions: list[ 2172 prediction_protein_info.PredictionProteinInfo 2173 ] = prediction_util.get_prediction_name_and_seq_from_table( 2174 self._view.ui.table_pred_analysis_multi_prot_to_predict, 2175 ) 2176 2177 self._active_task = tasks.Task( 2178 target=main_presenter_async.predict_protein_with_colabfold, 2179 args=( 2180 predictions, 2181 self.prediction_configuration, 2182 self._current_project, 2183 ), 2184 post_func=self.__await_multimer_prediction_for_subsequent_analysis, 2185 ) 2186 self._active_task.start() 2187 2188 self.block_box_prediction = QtWidgets.QMessageBox() 2189 self.block_box_prediction.setIcon(QtWidgets.QMessageBox.Information) 2190 self.block_box_prediction.setWindowIcon(QtGui.QIcon(constants.PLUGIN_LOGO_FILEPATH)) 2191 styles.set_stylesheet(self.block_box_prediction) 2192 self.block_box_prediction.setWindowTitle("Structure Prediction") 2193 self.block_box_prediction.setText("A prediction is currently running.") 2194 btn_abort = self.block_box_prediction.addButton("Abort", QtWidgets.QMessageBox.ActionRole) 2195 self.block_box_prediction.exec_() 2196 if self.block_box_prediction.clickedButton() == btn_abort: 2197 self.abort_prediction() 2198 self.block_box_prediction.close() 2199 self._view.wait_spinner.stop() 2200 else: 2201 self.block_box_prediction.close() 2202 self._view.wait_spinner.stop() 2203 2204 def __await_multimer_prediction_for_subsequent_analysis(self, result: tuple) -> None: 2205 tmp_exit_code = result[0] 2206 tmp_exit_code_description = [1] 2207 if tmp_exit_code == exit_codes.EXIT_CODE_ZERO[0]: 2208 # Prediction was successful 2209 self.block_box_prediction.destroy(True) 2210 constants.PYSSA_LOGGER.info("All structure predictions are done.") 2211 self.update_status("All structure predictions are done.") 2212 constants.PYSSA_LOGGER.info("Begin analysis process.") 2213 self.update_status("Begin analysis process ...") 2214 tmp_raw_analysis_run_names: list = [] 2215 for row_no in range(self._view.ui.list_pred_analysis_multi_overview.count()): 2216 tmp_raw_analysis_run_names.append(self._view.ui.list_pred_analysis_multi_overview.item(row_no).text()) 2217 2218 self._active_task = tasks.Task( 2219 target=main_presenter_async.run_distance_analysis, 2220 args=( 2221 tmp_raw_analysis_run_names, 2222 self._current_project, 2223 self._application_settings, 2224 self._view.ui.cb_pred_analysis_multi_images.isChecked(), 2225 ), 2226 post_func=self.post_analysis_process, 2227 ) 2228 self._active_task.start() 2229 2230 if not os.path.exists(constants.SCRATCH_DIR_ANALYSIS): 2231 os.mkdir(constants.SCRATCH_DIR_ANALYSIS) 2232 self.block_box_analysis.exec_() 2233 self.display_view_page() 2234 2235 elif tmp_exit_code == exit_codes.ERROR_WRITING_FASTA_FILES[0]: 2236 self.block_box_prediction.destroy(True) 2237 basic_boxes.ok( 2238 "Prediction", 2239 "Prediction failed because there was an error writing the fasta file(s)!", 2240 QtWidgets.QMessageBox.Critical, 2241 ) 2242 self.display_view_page() 2243 self._project_watcher.show_valid_options(self._view.ui) 2244 constants.PYSSA_LOGGER.error( 2245 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 2246 ) 2247 self._view.wait_spinner.stop() 2248 elif tmp_exit_code == exit_codes.ERROR_FASTA_FILES_NOT_FOUND[0]: 2249 self.block_box_prediction.destroy(True) 2250 basic_boxes.ok( 2251 "Prediction", 2252 "Prediction failed because the fasta file(s) could not be found!", 2253 QtWidgets.QMessageBox.Critical, 2254 ) 2255 self.display_view_page() 2256 self._project_watcher.show_valid_options(self._view.ui) 2257 constants.PYSSA_LOGGER.error( 2258 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 2259 ) 2260 self._view.wait_spinner.stop() 2261 elif tmp_exit_code == exit_codes.ERROR_PREDICTION_FAILED[0]: 2262 self.block_box_prediction.destroy(True) 2263 basic_boxes.ok( 2264 "Prediction", 2265 "Prediction failed because a subprocess failed!", 2266 QtWidgets.QMessageBox.Critical, 2267 ) 2268 self.display_view_page() 2269 self._project_watcher.show_valid_options(self._view.ui) 2270 constants.PYSSA_LOGGER.error( 2271 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 2272 ) 2273 self._view.wait_spinner.stop() 2274 elif tmp_exit_code == exit_codes.EXIT_CODE_ONE_UNKNOWN_ERROR[0]: 2275 self.block_box_prediction.destroy(True) 2276 basic_boxes.ok( 2277 "Prediction", 2278 "Prediction failed because of an unknown error!", 2279 QtWidgets.QMessageBox.Critical, 2280 ) 2281 self.display_view_page() 2282 self._project_watcher.show_valid_options(self._view.ui) 2283 constants.PYSSA_LOGGER.error( 2284 f"Prediction ended with exit code {tmp_exit_code}: {tmp_exit_code_description}", 2285 ) 2286 self._view.wait_spinner.stop() 2287 2288 def multi_pred_analysis_structure_analysis_next_2(self) -> None: 2289 """Shows the gui elements to select the chains in protein 1.""" 2290 self._view.wait_spinner.start() 2291 tmp_proteins_to_predict: list[str] = [] 2292 for i in range(self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount()): 2293 tmp_proteins_to_predict.append( 2294 self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem(i).text(), 2295 ) 2296 self._active_task = tasks.Task( 2297 target=main_presenter_async.check_chains_for_subsequent_analysis, 2298 args=( 2299 self._view.ui.box_pred_analysis_multi_prot_struct_1.currentText(), 2300 self._view.ui.box_pred_analysis_multi_prot_struct_2.currentText(), 2301 self._current_project, 2302 tmp_proteins_to_predict, 2303 ), 2304 post_func=self.__await_multi_pred_analysis_structure_analysis_next_2, 2305 ) 2306 self._active_task.start() 2307 2308 def __await_multi_pred_analysis_structure_analysis_next_2(self, result: tuple) -> None: 2309 # fixme: something is not quite right with the detection of the chains! 2310 _, tmp_analysis_name = result 2311 if tmp_analysis_name != "": 2312 gui_elements_to_show = [ 2313 self._view.ui.btn_pred_analysis_multi_remove, 2314 self._view.ui.btn_pred_analysis_multi_add, 2315 self._view.ui.lbl_pred_analysis_multi_overview, 2316 self._view.ui.list_pred_analysis_multi_overview, 2317 self._view.ui.lbl_pred_analysis_multi_images, 2318 self._view.ui.cb_pred_analysis_multi_images, 2319 self._view.ui.btn_pred_analysis_multi_start, 2320 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 2321 ] 2322 gui_elements_to_hide = [ 2323 self._view.ui.box_pred_analysis_multi_prot_struct_1, 2324 self._view.ui.box_pred_analysis_multi_prot_struct_2, 2325 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 2326 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 2327 self._view.ui.lbl_analysis_batch_vs_3, 2328 self._view.ui.lbl_pred_analysis_multi_ref_chains, 2329 self._view.ui.list_pred_analysis_multi_ref_chains, 2330 self._view.ui.lbl_pred_analysis_multi_model_chains, 2331 self._view.ui.list_pred_analysis_multi_model_chains, 2332 self._view.ui.btn_pred_analysis_multi_back_3, 2333 self._view.ui.btn_pred_analysis_multi_next_2, 2334 self._view.ui.btn_pred_analysis_multi_back_4, 2335 self._view.ui.btn_pred_analysis_multi_next_3, 2336 self._view.ui.btn_pred_analysis_multi_back_5, 2337 self._view.ui.btn_pred_analysis_multi_next_4, 2338 ] 2339 gui_utils.show_gui_elements(gui_elements_to_show) 2340 gui_utils.hide_gui_elements(gui_elements_to_hide) 2341 item = QtWidgets.QListWidgetItem(tmp_analysis_name) 2342 self._view.ui.list_pred_analysis_multi_overview.addItem(item) 2343 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(False) 2344 else: 2345 gui_elements_to_show = [ 2346 self._view.ui.lbl_pred_analysis_multi_overview, 2347 self._view.ui.list_pred_analysis_multi_overview, 2348 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 2349 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 2350 self._view.ui.lbl_analysis_batch_vs_3, 2351 self._view.ui.lbl_pred_analysis_multi_ref_chains, 2352 self._view.ui.list_pred_analysis_multi_ref_chains, 2353 self._view.ui.btn_pred_analysis_multi_back_4, 2354 self._view.ui.btn_pred_analysis_multi_next_3, 2355 ] 2356 gui_elements_to_hide = [ 2357 self._view.ui.btn_pred_analysis_multi_remove, 2358 self._view.ui.btn_pred_analysis_multi_add, 2359 self._view.ui.box_pred_analysis_multi_prot_struct_1, 2360 self._view.ui.box_pred_analysis_multi_prot_struct_2, 2361 self._view.ui.btn_pred_analysis_multi_back_3, 2362 self._view.ui.btn_pred_analysis_multi_next_2, 2363 self._view.ui.lbl_pred_analysis_multi_model_chains, 2364 self._view.ui.list_pred_analysis_multi_model_chains, 2365 self._view.ui.btn_pred_analysis_multi_back_5, 2366 self._view.ui.btn_pred_analysis_multi_next_4, 2367 self._view.ui.lbl_pred_analysis_multi_images, 2368 self._view.ui.cb_pred_analysis_multi_images, 2369 self._view.ui.btn_pred_analysis_multi_start, 2370 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 2371 ] 2372 gui_utils.show_gui_elements(gui_elements_to_show) 2373 gui_utils.hide_gui_elements(gui_elements_to_hide) 2374 self._view.ui.lbl_pred_analysis_multi_prot_struct_1.setText( 2375 self._view.ui.box_pred_analysis_multi_prot_struct_1.currentText(), 2376 ) 2377 self._view.ui.lbl_pred_analysis_multi_prot_struct_2.setText( 2378 self._view.ui.box_pred_analysis_multi_prot_struct_2.currentText(), 2379 ) 2380 self._view.ui.list_pred_analysis_multi_ref_chains.clear() 2381 self._view.ui.btn_pred_analysis_multi_next_3.setEnabled(False) 2382 self._view.ui.list_pred_analysis_multi_ref_chains.setEnabled(True) 2383 2384 for i in range(self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount()): 2385 if ( 2386 self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem(i).text() 2387 == self._view.ui.box_pred_analysis_multi_prot_struct_1.currentText() 2388 ): 2389 self._view.ui.list_pred_analysis_multi_ref_chains.addItem( 2390 self._view.ui.table_pred_analysis_multi_prot_to_predict.item(i, 0).text(), 2391 ) 2392 if self._view.ui.list_pred_analysis_multi_ref_chains.count() == 0: 2393 tmp_protein = self._current_project.search_protein( 2394 self._view.ui.box_pred_analysis_multi_prot_struct_1.currentText(), 2395 ) 2396 for tmp_chain in tmp_protein.chains: 2397 if tmp_chain.chain_type == "protein_chain": 2398 self._view.ui.list_pred_analysis_multi_ref_chains.addItem(tmp_chain.chain_letter) 2399 if self._view.ui.list_pred_analysis_multi_ref_chains.count() == 1: 2400 self._view.ui.lbl_pred_analysis_multi_ref_chains.setText( 2401 f"Select chain in protein structure {self._view.ui.lbl_pred_analysis_multi_prot_struct_1.text()}.", 2402 ) 2403 else: 2404 self._view.ui.lbl_pred_analysis_multi_ref_chains.setText( 2405 f"Select chains in protein structure {self._view.ui.lbl_pred_analysis_multi_prot_struct_1.text()}.", 2406 ) 2407 self._view.wait_spinner.stop() 2408 2409 # </editor-fold> 2410 2411 # <editor-fold desc="Structure Analysis functions"> 2412 def post_analysis_process(self, an_exit_code: tuple[int, str]) -> None: 2413 """Post process after the analysis thread finished.""" 2414 constants.PYSSA_LOGGER.debug("post_analysis_process() started ...") 2415 if an_exit_code[0] == exit_codes.ERROR_DISTANCE_ANALYSIS_FAILED[0]: 2416 self.block_box_analysis.destroy(True) 2417 basic_boxes.ok( 2418 "Distance analysis", 2419 "Distance analysis failed because there was an error during the analysis!", 2420 QtWidgets.QMessageBox.Critical, 2421 ) 2422 constants.PYSSA_LOGGER.error( 2423 f"Distance analysis ended with exit code {an_exit_code[0]}: {an_exit_code[1]}", 2424 ) 2425 elif an_exit_code[0] == exit_codes.EXIT_CODE_ONE_UNKNOWN_ERROR[0]: 2426 self.block_box_analysis.destroy(True) 2427 basic_boxes.ok( 2428 "Distance analysis", 2429 "Distance analysis failed because of an unknown error!", 2430 QtWidgets.QMessageBox.Critical, 2431 ) 2432 constants.PYSSA_LOGGER.error( 2433 f"Distance analysis ended with exit code {an_exit_code[0]}: {an_exit_code[1]}", 2434 ) 2435 elif an_exit_code[0] == exit_codes.EXIT_CODE_ZERO[0]: 2436 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 2437 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 2438 self.block_box_analysis.destroy(True) 2439 basic_boxes.ok( 2440 "Structure analysis", 2441 "All structure analysis' are done. Go to results to check the new results.", 2442 QtWidgets.QMessageBox.Information, 2443 ) 2444 constants.PYSSA_LOGGER.info("All structure analysis' are done.") 2445 2446 self._project_watcher.show_valid_options(self._view.ui) 2447 self.display_view_page() 2448 self._init_batch_analysis_page() 2449 2450 def start_process_batch(self) -> None: 2451 """Sets up the worker for the analysis task.""" 2452 constants.PYSSA_LOGGER.info("Begin analysis process.") 2453 2454 tmp_raw_analysis_run_names: list = [] 2455 for row_no in range(self._view.ui.list_analysis_batch_overview.count()): 2456 tmp_raw_analysis_run_names.append(self._view.ui.list_analysis_batch_overview.item(row_no).text()) 2457 self._active_task = tasks.Task( 2458 target=main_presenter_async.run_distance_analysis, 2459 args=( 2460 tmp_raw_analysis_run_names, 2461 self._current_project, 2462 self._application_settings, 2463 self._view.ui.cb_analysis_images.isChecked(), 2464 ), 2465 post_func=self.post_analysis_process, 2466 ) 2467 self._active_task.start() 2468 2469 if not os.path.exists(constants.SCRATCH_DIR_ANALYSIS): 2470 os.mkdir(constants.SCRATCH_DIR_ANALYSIS) 2471 2472 self.block_box_analysis.exec_() 2473 self.display_view_page() 2474 2475 def structure_analysis_next(self) -> None: 2476 """Shows the gui elements to select the chains in protein 1.""" 2477 self._view.wait_spinner.start() 2478 self._active_task = tasks.Task( 2479 target=main_presenter_async.check_chains_for_analysis, 2480 args=( 2481 self._view.ui.box_analysis_batch_prot_struct_1.currentText(), 2482 self._view.ui.box_analysis_batch_prot_struct_2.currentText(), 2483 self._current_project, 2484 ), 2485 post_func=self.__await_structure_analysis_next, 2486 ) 2487 self._active_task.start() 2488 2489 def __await_structure_analysis_next(self, result: tuple) -> None: 2490 _, tmp_is_only_one_chain, tmp_analysis_run_name, tmp_protein_1, tmp_protein_2 = result 2491 2492 if tmp_is_only_one_chain: 2493 gui_elements_to_show = [ 2494 self._view.ui.btn_analysis_batch_remove, 2495 self._view.ui.btn_analysis_batch_add, 2496 self._view.ui.lbl_analysis_batch_overview, 2497 self._view.ui.list_analysis_batch_overview, 2498 self._view.ui.lbl_analysis_batch_images, 2499 self._view.ui.cb_analysis_batch_images, 2500 self._view.ui.btn_analysis_batch_start, 2501 ] 2502 gui_elements_to_hide = [ 2503 self._view.ui.box_analysis_batch_prot_struct_1, 2504 self._view.ui.box_analysis_batch_prot_struct_2, 2505 self._view.ui.lbl_analysis_batch_prot_struct_1, 2506 self._view.ui.lbl_analysis_batch_prot_struct_2, 2507 self._view.ui.lbl_analysis_batch_vs, 2508 self._view.ui.lbl_analysis_batch_ref_chains, 2509 self._view.ui.list_analysis_batch_ref_chains, 2510 self._view.ui.lbl_analysis_batch_model_chains, 2511 self._view.ui.list_analysis_batch_model_chains, 2512 self._view.ui.btn_analysis_batch_back, 2513 self._view.ui.btn_analysis_batch_next, 2514 self._view.ui.btn_analysis_batch_back_2, 2515 self._view.ui.btn_analysis_batch_next_2, 2516 self._view.ui.btn_analysis_batch_back_3, 2517 self._view.ui.btn_analysis_batch_next_3, 2518 ] 2519 gui_utils.show_gui_elements(gui_elements_to_show) 2520 gui_utils.hide_gui_elements(gui_elements_to_hide) 2521 item = QtWidgets.QListWidgetItem(tmp_analysis_run_name) 2522 self._view.ui.list_analysis_batch_overview.addItem(item) 2523 self._view.ui.btn_analysis_batch_remove.setEnabled(False) 2524 else: 2525 gui_elements_to_show = [ 2526 self._view.ui.lbl_analysis_batch_overview, 2527 self._view.ui.list_analysis_batch_overview, 2528 self._view.ui.lbl_analysis_batch_prot_struct_1, 2529 self._view.ui.lbl_analysis_batch_prot_struct_2, 2530 self._view.ui.lbl_analysis_batch_vs, 2531 self._view.ui.lbl_analysis_batch_ref_chains, 2532 self._view.ui.list_analysis_batch_ref_chains, 2533 self._view.ui.btn_analysis_batch_back_2, 2534 self._view.ui.btn_analysis_batch_next_2, 2535 ] 2536 gui_elements_to_hide = [ 2537 self._view.ui.btn_analysis_batch_remove, 2538 self._view.ui.btn_analysis_batch_add, 2539 self._view.ui.box_analysis_batch_prot_struct_1, 2540 self._view.ui.box_analysis_batch_prot_struct_2, 2541 self._view.ui.btn_analysis_batch_back, 2542 self._view.ui.btn_analysis_batch_next, 2543 self._view.ui.lbl_analysis_batch_model_chains, 2544 self._view.ui.list_analysis_batch_model_chains, 2545 self._view.ui.btn_analysis_batch_back_3, 2546 self._view.ui.btn_analysis_batch_next_3, 2547 self._view.ui.lbl_analysis_batch_images, 2548 self._view.ui.cb_analysis_batch_images, 2549 self._view.ui.btn_analysis_batch_start, 2550 ] 2551 gui_utils.show_gui_elements(gui_elements_to_show) 2552 gui_utils.hide_gui_elements(gui_elements_to_hide) 2553 self._view.ui.lbl_analysis_batch_prot_struct_1.setText( 2554 self._view.ui.box_analysis_batch_prot_struct_1.currentText(), 2555 ) 2556 self._view.ui.lbl_analysis_batch_prot_struct_2.setText( 2557 self._view.ui.box_analysis_batch_prot_struct_2.currentText(), 2558 ) 2559 self._view.ui.list_analysis_batch_ref_chains.clear() 2560 self._view.ui.btn_analysis_batch_next_2.setEnabled(False) 2561 self._view.ui.list_analysis_batch_ref_chains.setEnabled(True) 2562 2563 for tmp_chain in tmp_protein_1.chains: 2564 if tmp_chain.chain_type == "protein_chain": 2565 self._view.ui.list_analysis_batch_ref_chains.addItem(tmp_chain.chain_letter) 2566 2567 if self._view.ui.list_analysis_batch_ref_chains.count() == 1: 2568 self._view.ui.lbl_analysis_batch_ref_chains.setText( 2569 f"Select chain in protein structure {self._view.ui.lbl_analysis_batch_prot_struct_1.text()}.", 2570 ) 2571 else: 2572 self._view.ui.lbl_analysis_batch_ref_chains.setText( 2573 f"Select chains in protein structure {self._view.ui.lbl_analysis_batch_prot_struct_1.text()}.", 2574 ) 2575 self._view.wait_spinner.stop() 2576 2577 # </editor-fold> 2578 2579 # <editor-fold desc="Analysis Images"> 2580 def post_image_creation_process(self) -> None: 2581 """Post method after the image creation task is finished.""" 2582 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 2583 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 2584 self.block_box_images.destroy(True) 2585 basic_boxes.ok( 2586 "Analysis Images", 2587 "All images of all analysis' have been created. Go to results to check the new results.", 2588 QtWidgets.QMessageBox.Information, 2589 ) 2590 constants.PYSSA_LOGGER.info("All images of all analysis' have been created.") 2591 self._init_analysis_image_page() 2592 self.display_view_page() 2593 self._project_watcher.show_valid_options(self._view.ui) 2594 2595 def start_automatic_image_creation(self) -> None: 2596 """Sets up the worker for the image creation process.""" 2597 constants.PYSSA_LOGGER.info("Begin image creation process.") 2598 # self.worker_image_creation = workers.BatchImageWorkerPool( 2599 # self._view.ui.list_analysis_images_struct_analysis, self._view.ui.list_analysis_images_creation_struct_analysis, 2600 # self._view.status_bar, self._current_project) 2601 constants.PYSSA_LOGGER.info("Thread started for image creation process.") 2602 # self.threadpool.start(self.worker_image_creation) 2603 2604 # <editor-fold desc="Worker setup"> 2605 # TODO: test code below 2606 # --Begin: worker setup 2607 self.tmp_thread = QtCore.QThread() 2608 self.tmp_worker = task_workers.BatchImageWorker( 2609 self._view.ui.list_analysis_images_struct_analysis, 2610 self._view.ui.list_analysis_images_creation_struct_analysis, 2611 self._view.status_bar, 2612 self._current_project, 2613 ) 2614 self.tmp_thread = task_workers.setup_worker_for_work(self.tmp_thread, self.tmp_worker, self.display_view_page) 2615 self.tmp_worker.finished.connect(self.post_image_creation_process) 2616 self.tmp_thread.start() 2617 # --End: worker setup 2618 2619 # </editor-fold> 2620 2621 if not os.path.exists(constants.SCRATCH_DIR_ANALYSIS): 2622 os.mkdir(constants.SCRATCH_DIR_ANALYSIS) 2623 2624 self._view.ui.list_analysis_images_struct_analysis.setEnabled(False) 2625 self._view.ui.list_analysis_images_creation_struct_analysis.setEnabled(False) 2626 2627 # gui_elements_to_show = [ 2628 # self._view.ui.btn_analysis_abort, 2629 # ] 2630 # gui_elements_to_hide = [ 2631 # self._view.ui.btn_save_project, 2632 # self._view.ui.btn_edit_page, 2633 # self._view.ui.btn_view_page, 2634 # self._view.ui.btn_use_page, 2635 # self._view.ui.btn_export_project, 2636 # self._view.ui.btn_close_project, 2637 # self._view.ui.btn_batch_analysis_page, 2638 # self._view.ui.btn_image_analysis_page, 2639 # self._view.ui.btn_results_page, 2640 # self._view.ui.lbl_handle_pymol_session, 2641 # self._view.ui.btn_image_page, 2642 # self._view.ui.btn_hotspots_page, 2643 # ] 2644 # gui_utils.manage_gui_visibility(gui_elements_to_show, gui_elements_to_hide) 2645 2646 self.block_box_images.exec_() 2647 2648 # </editor-fold> 2649 2650 # <editor-fold desc="Results page functions"> 2651 def show_analysis_results_options(self) -> None: 2652 """Shows the combo box of protein pairs.""" 2653 self.results_management.show_stage_x(0) 2654 2655 def show_results_interactions(self, gui_elements_to_show: list = None, gui_elements_to_hide: list = None) -> None: 2656 """Shows the gui elements of the results page. 2657 2658 Args: 2659 gui_elements_to_show: a list of gui elements which should get displayed. 2660 gui_elements_to_hide: a list of gui elements which should get hidden. 2661 """ 2662 if gui_elements_to_hide is not None: 2663 self.results_management.show_gui_elements_stage_x( 2664 [0, 1], 2665 [], 2666 show_specific_elements=[ 2667 self._view.ui.lbl_results_analysis_options, 2668 self._view.ui.cb_results_analysis_options, 2669 ], 2670 hide_specific_elements=gui_elements_to_hide, 2671 ) 2672 else: 2673 self.results_management.show_gui_elements_stage_x( 2674 [0, 1], 2675 [], 2676 show_specific_elements=[ 2677 self._view.ui.lbl_results_analysis_options, 2678 self._view.ui.cb_results_analysis_options, 2679 ], 2680 ) 2681 2682 def load_results(self) -> None: 2683 """Sets up the worker for the result loading process.""" 2684 self._view.wait_spinner.start() 2685 if self.is_distance_plot_open: 2686 self.distance_plot_dialog.close() 2687 self.is_distance_plot_open = False 2688 self.results_name = self._view.ui.cb_results_analysis_options.currentText() 2689 if self.results_name == "": 2690 self.show_analysis_results_options() 2691 self._view.wait_spinner.stop() 2692 return 2693 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 2694 2695 self._active_task = tasks.Task( 2696 target=main_presenter_async.load_results, 2697 args=( 2698 self._current_project, 2699 self.results_name, 2700 ), 2701 post_func=self.__await_load_results, 2702 ) 2703 self._active_task.start() 2704 2705 self._view.ui.list_results_interest_regions.clear() 2706 self._view.status_bar.showMessage(f"Loading results of {self.results_name} ...") 2707 2708 def __await_load_results(self, result: tuple) -> None: 2709 _, images_type, self.current_session, tmp_rmsd, tmp_no_aligned_residues = result 2710 2711 if images_type == constants.IMAGES_ALL: 2712 gui_elements_to_show = [ 2713 self._view.ui.lbl_results_analysis_options, 2714 self._view.ui.cb_results_analysis_options, 2715 self._view.ui.lbl_results_rmsd, 2716 self._view.ui.txt_results_rmsd, 2717 self._view.ui.lbl_color_rmsd, 2718 self._view.ui.btn_color_rmsd, 2719 self._view.ui.lbl_results_aligned_residues, 2720 self._view.ui.txt_results_aligned_residues, 2721 self._view.ui.lbl_results_distance_plot, 2722 self._view.ui.btn_view_distance_plot, 2723 self._view.ui.lbl_results_distance_histogram, 2724 self._view.ui.btn_view_distance_histogram, 2725 self._view.ui.lbl_results_distance_table, 2726 self._view.ui.btn_view_distance_table, 2727 self._view.ui.lbl_results_structure_alignment, 2728 self._view.ui.btn_view_struct_alignment, 2729 self._view.ui.lbl_results_interest_regions, 2730 self._view.ui.list_results_interest_regions, 2731 self._view.ui.btn_view_interesting_region, 2732 ] 2733 gui_utils.show_gui_elements(gui_elements_to_show) 2734 for tmp_filename in os.listdir(constants.CACHE_STRUCTURE_ALN_IMAGES_INTERESTING_REGIONS_DIR): 2735 self._view.ui.list_results_interest_regions.addItem(tmp_filename) 2736 self._view.ui.list_results_interest_regions.sortItems() 2737 elif images_type == constants.IMAGES_STRUCT_ALN_ONLY: 2738 gui_elements_to_show = [ 2739 self._view.ui.lbl_results_analysis_options, 2740 self._view.ui.cb_results_analysis_options, 2741 self._view.ui.lbl_results_rmsd, 2742 self._view.ui.txt_results_rmsd, 2743 self._view.ui.lbl_color_rmsd, 2744 self._view.ui.btn_color_rmsd, 2745 self._view.ui.lbl_results_aligned_residues, 2746 self._view.ui.txt_results_aligned_residues, 2747 self._view.ui.lbl_results_distance_plot, 2748 self._view.ui.btn_view_distance_plot, 2749 self._view.ui.lbl_results_distance_histogram, 2750 self._view.ui.btn_view_distance_histogram, 2751 self._view.ui.lbl_results_distance_table, 2752 self._view.ui.btn_view_distance_table, 2753 self._view.ui.lbl_results_structure_alignment, 2754 self._view.ui.btn_view_struct_alignment, 2755 ] 2756 gui_elements_to_hide = [ 2757 self._view.ui.lbl_results_interest_regions, 2758 self._view.ui.list_results_interest_regions, 2759 self._view.ui.btn_view_interesting_region, 2760 ] 2761 gui_utils.show_gui_elements(gui_elements_to_show) 2762 gui_utils.hide_gui_elements(gui_elements_to_hide) 2763 self._view.ui.list_results_interest_regions.sortItems() 2764 elif images_type == constants.IMAGES_NONE: 2765 gui_elements_to_show = [ 2766 self._view.ui.lbl_results_analysis_options, 2767 self._view.ui.cb_results_analysis_options, 2768 self._view.ui.lbl_results_rmsd, 2769 self._view.ui.txt_results_rmsd, 2770 self._view.ui.lbl_color_rmsd, 2771 self._view.ui.btn_color_rmsd, 2772 self._view.ui.lbl_results_aligned_residues, 2773 self._view.ui.txt_results_aligned_residues, 2774 self._view.ui.lbl_results_distance_plot, 2775 self._view.ui.btn_view_distance_plot, 2776 self._view.ui.lbl_results_distance_histogram, 2777 self._view.ui.btn_view_distance_histogram, 2778 self._view.ui.lbl_results_distance_table, 2779 self._view.ui.btn_view_distance_table, 2780 ] 2781 gui_elements_to_hide = [ 2782 self._view.ui.lbl_results_structure_alignment, 2783 self._view.ui.btn_view_struct_alignment, 2784 self._view.ui.lbl_results_interest_regions, 2785 self._view.ui.list_results_interest_regions, 2786 self._view.ui.btn_view_interesting_region, 2787 ] 2788 gui_utils.show_gui_elements(gui_elements_to_show) 2789 gui_utils.hide_gui_elements(gui_elements_to_hide) 2790 else: 2791 raise ValueError("Illegal argument.") 2792 2793 self._view.ui.txt_results_rmsd.setText(str(tmp_rmsd)) 2794 self._view.ui.txt_results_aligned_residues.setText(str(tmp_no_aligned_residues)) 2795 self._view.status_bar.showMessage(f"Current workspace: {str(self._workspace_path)}") 2796 self.main_window_state.results_page.results_name = self._view.ui.cb_results_analysis_options.currentText() 2797 self._view.wait_spinner.stop() 2798 2799 def color_protein_pair_by_rmsd(self) -> None: 2800 """Colors the residues in 5 colors depending on their distance to the reference.""" 2801 self._view.wait_spinner.start() 2802 self._active_task = tasks.Task( 2803 target=main_presenter_async.color_protein_pair_by_rmsd_value, 2804 args=( 2805 self._current_project, 2806 self.results_name, 2807 ), 2808 post_func=self.__await_color_protein_pair_by_rmsd, 2809 ) 2810 self._active_task.start() 2811 self._view.status_bar.showMessage("Coloring protein pair by RMSD value ...") 2812 # hide unnecessary representations 2813 # fixme: it might be a problem to hide any representation at this point 2814 # cmd.hide("cartoon", tmp_protein_pair.protein_1.get_molecule_object()) 2815 # cmd.hide("cartoon", f"{tmp_protein_pair.protein_2.get_molecule_object()}") 2816 # cmd.hide("cartoon", f"{tmp_protein_pair.protein_2.get_molecule_object()}") 2817 2818 def __await_color_protein_pair_by_rmsd(self, result: tuple) -> None: 2819 self._view.wait_spinner.stop() 2820 2821 # </editor-fold> 2822 2823 # <editor-fold desc="Display page functions"> 2824 def display_structure_alignment(self) -> None: 2825 """Opens a window which displays the image of the structure alignment.""" 2826 png_dialog = QtWidgets.QDialog(self._view) 2827 label = QtWidgets.QLabel(self._view) 2828 pathlib.Path( 2829 f"{self._workspace_path}/{self._view.ui.lbl_current_project_name.text()}/results/{self.results_name}", 2830 ) 2831 self._view.ui.cb_results_analysis_options.currentText() 2832 pixmap = QtGui.QPixmap( 2833 f"{constants.CACHE_STRUCTURE_ALN_IMAGES_DIR}/structure_aln_{self._view.ui.cb_results_analysis_options.currentText()}", 2834 ) 2835 # TO-DO: Create setting for min. image size 2836 pixmap = pixmap.scaled(450, 450, transformMode=QtCore.Qt.SmoothTransformation) 2837 label.setPixmap(pixmap) 2838 label.setScaledContents(True) 2839 png_dialog_layout = QtWidgets.QHBoxLayout() 2840 png_dialog_layout.addWidget(label) 2841 png_dialog.setLayout(png_dialog_layout) 2842 png_dialog.setWindowTitle("Image of: structure alignment") 2843 png_dialog.show() 2844 2845 def display_distance_plot(self) -> None: 2846 """Opens a window which displays the distance plot.""" 2847 protein_pair_of_analysis = self._current_project.search_protein_pair( 2848 self._view.ui.cb_results_analysis_options.currentText(), 2849 ) 2850 2851 tmp_dialog = plot_view.PlotView(protein_pair_of_analysis, self._current_project, self._view.ui.cb_results_analysis_options.currentText()) 2852 tmp_dialog.exec_() 2853 2854 # self.distance_plot_dialog = dialog_distance_plot.DialogDistancePlot(protein_pair_of_analysis, self._current_project, 2855 # self._view.ui.cb_results_analysis_options.currentText()) 2856 # self.distance_plot_dialog.setWindowModality(Qt.WindowModal) 2857 # self.is_distance_plot_open = True 2858 # self.distance_plot_dialog.exec_() 2859 2860 def display_distance_histogram(self) -> None: 2861 """Opens a window which displays the distance histogram.""" 2862 if self.is_distance_plot_open: 2863 self.distance_plot_dialog.close() 2864 self.is_distance_plot_open = False 2865 protein_pair_of_analysis = self._current_project.search_protein_pair( 2866 self._view.ui.cb_results_analysis_options.currentText(), 2867 ) 2868 dialog = dialog_distance_histogram.DialogDistanceHistogram(protein_pair_of_analysis) 2869 dialog.exec_() 2870 2871 def display_interesting_region(self) -> None: 2872 """Displays an image of an interesting region.""" 2873 if self.is_distance_plot_open: 2874 self.distance_plot_dialog.close() 2875 self.is_distance_plot_open = False 2876 png_dialog = QtWidgets.QDialog(self._view) 2877 label = QtWidgets.QLabel(self._view) 2878 file_name = self._view.ui.list_results_interest_regions.currentItem().text() 2879 pixmap = QtGui.QPixmap(f"{constants.CACHE_STRUCTURE_ALN_IMAGES_INTERESTING_REGIONS_DIR}/{file_name}") 2880 # TODO: Create setting for min. image size 2881 pixmap = pixmap.scaled(450, 450, transformMode=QtCore.Qt.SmoothTransformation) 2882 label.setPixmap(pixmap) 2883 label.setScaledContents(True) 2884 png_dialog_layout = QtWidgets.QHBoxLayout() 2885 png_dialog_layout.addWidget(label) 2886 png_dialog.setLayout(png_dialog_layout) 2887 png_dialog.setWindowTitle(f"Image of: {file_name}") 2888 png_dialog.show() 2889 2890 def display_distance_table(self) -> None: 2891 """Displays the distances in a table.""" 2892 if self.is_distance_plot_open: 2893 self.distance_plot_dialog.close() 2894 self.is_distance_plot_open = False 2895 csv_model = QtGui.QStandardItemModel() 2896 csv_model.setColumnCount(7) 2897 labels = [ 2898 "Residue pair no.", 2899 "Protein 1 Chain", 2900 "Protein 1 Position", 2901 "Protein 1 Residue", 2902 "Protein 2 Chain", 2903 "Protein 2 Position", 2904 "Protein 2 Residue", 2905 "Distance in Å", 2906 ] 2907 csv_model.setHorizontalHeaderLabels(labels) 2908 table_dialog = QtWidgets.QDialog(self._view) 2909 table_view = QtWidgets.QTableView() 2910 table_view.setModel(csv_model) 2911 2912 tmp_protein_pair = self._current_project.search_protein_pair( 2913 self._view.ui.cb_results_analysis_options.currentText(), 2914 ) 2915 csv_filepath = pathlib.Path(f"{constants.CACHE_CSV_DIR}/{tmp_protein_pair.name}.csv") 2916 if not os.path.exists(constants.CACHE_CSV_DIR): 2917 os.mkdir(constants.CACHE_CSV_DIR) 2918 tmp_protein_pair = self._current_project.search_protein_pair(self.results_name) 2919 2920 distance_data = tmp_protein_pair.distance_analysis.analysis_results.distance_data 2921 distance_data_array = np.array( 2922 [ 2923 distance_data[pyssa_keys.ARRAY_DISTANCE_INDEX], 2924 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_1_CHAIN], 2925 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_1_POSITION], 2926 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_1_RESI], 2927 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_2_CHAIN], 2928 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_2_POSITION], 2929 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_2_RESI], 2930 distance_data[pyssa_keys.ARRAY_DISTANCE_DISTANCES], 2931 ], 2932 ) 2933 distance_data_array_transpose = distance_data_array.transpose() 2934 with open(csv_filepath, mode="w", newline="") as file: 2935 writer = csv.writer(file, delimiter=",") 2936 writer.writerows(distance_data_array_transpose) 2937 2938 file.close() 2939 2940 with open(csv_filepath, "r", encoding="utf-8") as csv_file: 2941 i = 0 2942 for line in csv_file: 2943 tmp_list = line.split(",") 2944 # tmp_list.pop(0) 2945 standard_item_list = [] 2946 pair_no_item = QtGui.QStandardItem() 2947 pair_no_item.setData(int(tmp_list[0]), role=QtCore.Qt.DisplayRole) 2948 ref_chain_item = QtGui.QStandardItem() 2949 ref_chain_item.setData(str(tmp_list[1]), role=QtCore.Qt.DisplayRole) 2950 ref_pos_item = QtGui.QStandardItem() 2951 ref_pos_item.setData(int(tmp_list[2]), role=QtCore.Qt.DisplayRole) 2952 ref_resi_item = QtGui.QStandardItem() 2953 ref_resi_item.setData(str(tmp_list[3]), role=QtCore.Qt.DisplayRole) 2954 model_chain_item = QtGui.QStandardItem() 2955 model_chain_item.setData(str(tmp_list[4]), role=QtCore.Qt.DisplayRole) 2956 model_pos_item = QtGui.QStandardItem() 2957 model_pos_item.setData(int(tmp_list[5]), role=QtCore.Qt.DisplayRole) 2958 model_resi_item = QtGui.QStandardItem() 2959 model_resi_item.setData(str(tmp_list[6]), role=QtCore.Qt.DisplayRole) 2960 distance_item = QtGui.QStandardItem() 2961 distance_item.setData(float(tmp_list[7]), role=QtCore.Qt.DisplayRole) 2962 standard_item_list.append(pair_no_item) 2963 standard_item_list.append(ref_chain_item) 2964 standard_item_list.append(ref_pos_item) 2965 standard_item_list.append(ref_resi_item) 2966 standard_item_list.append(model_chain_item) 2967 standard_item_list.append(model_pos_item) 2968 standard_item_list.append(model_resi_item) 2969 standard_item_list.append(distance_item) 2970 csv_model.insertRow(i, standard_item_list) 2971 i += 1 2972 csv_file.close() 2973 csv_model.removeRow(0) 2974 table_view.setAlternatingRowColors(True) 2975 table_view.resizeColumnsToContents() 2976 table_view.verticalHeader().setVisible(False) 2977 table_view.setSortingEnabled(True) 2978 table_view.sortByColumn(0, QtCore.Qt.AscendingOrder) 2979 table_dialog_layout = QtWidgets.QHBoxLayout() 2980 table_dialog_layout.addWidget(table_view) 2981 table_dialog.setLayout(table_dialog_layout) 2982 # styles 2983 stylesheet = """ 2984 QDialog {background-color: #F6F4F8;} 2985 QTableView {background-color: white;} 2986 """ 2987 table_dialog.setStyleSheet(stylesheet) 2988 table_dialog.setWindowFlag(QtCore.Qt.WindowMaximizeButtonHint, True) 2989 table_dialog.setWindowFlag(QtCore.Qt.WindowCloseButtonHint, True) 2990 table_dialog.setModal(True) 2991 table_view.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers) # disables editing of cells 2992 table_dialog.setWindowTitle("Distances of Structure Alignment") 2993 table_dialog.show() 2994 2995 # </editor-fold> 2996 2997 # <editor-fold desc="Manage page functions"> 2998 def choose_manage_open_protein(self) -> None: 2999 """Shows the different configuration gui elements.""" 3000 if self._view.ui.box_manage_choose_protein.currentText() != "": 3001 gui_elements_to_show = [ 3002 self._view.ui.lbl_manage_choose_color, 3003 self._view.ui.box_manage_choose_color, 3004 self._view.ui.lbl_manage_choose_representation, 3005 self._view.ui.box_manage_choose_representation, 3006 self._view.ui.lbl_manage_choose_bg_color, 3007 self._view.ui.box_manage_choose_bg_color, 3008 ] 3009 gui_utils.show_gui_elements(gui_elements_to_show) 3010 tmp_pymol_selection_option: str = "byres (resn CYS and name SG) within 2 of (resn CYS and name SG)" 3011 if ( 3012 cmd.select( 3013 name="disulfides", 3014 selection=f"{self._view.ui.box_manage_choose_protein.currentText()} & {tmp_pymol_selection_option}", 3015 ) 3016 > 0 3017 ): 3018 gui_elements_to_show = [ 3019 self._view.ui.lbl_disulfid_bond_1, 3020 self._view.ui.lbl_disulfid_bond_2, 3021 self._view.ui.btn_disulfid_bond_show, 3022 self._view.ui.btn_disulfid_bond_hide, 3023 ] 3024 gui_utils.show_gui_elements(gui_elements_to_show) 3025 else: 3026 gui_elements_to_hide = [ 3027 self._view.ui.lbl_manage_choose_color, 3028 self._view.ui.box_manage_choose_color, 3029 self._view.ui.lbl_manage_choose_representation, 3030 self._view.ui.box_manage_choose_representation, 3031 self._view.ui.lbl_manage_choose_bg_color, 3032 self._view.ui.box_manage_choose_bg_color, 3033 self._view.ui.lbl_disulfid_bond_1, 3034 self._view.ui.lbl_disulfid_bond_2, 3035 self._view.ui.btn_disulfid_bond_show, 3036 self._view.ui.btn_disulfid_bond_hide, 3037 ] 3038 gui_utils.hide_gui_elements(gui_elements_to_hide) 3039 3040 def choose_manage_color_selected_protein(self) -> None: 3041 """Sets the protein color.""" 3042 tmp_input = self._view.ui.box_manage_choose_protein.currentText() 3043 tmp_protein = self._current_project.search_protein(tmp_input) 3044 tmp_protein.color_protein_in_pymol( 3045 self._view.ui.box_manage_choose_color.currentText(), 3046 f"/{tmp_protein.get_molecule_object()}", 3047 ) 3048 3049 def choose_manage_representation(self) -> None: 3050 """Sets the representation.""" 3051 tmp_input = self._view.ui.box_manage_choose_protein.currentText() 3052 tmp_protein = self._current_project.search_protein(tmp_input) 3053 tmp_selection = f"/{tmp_protein.get_molecule_object()}" 3054 if self._view.ui.box_manage_choose_representation.currentIndex() == 0: 3055 print("Please select a representation.") 3056 self._view.status_bar.showMessage("Please select a representation.") 3057 elif self._view.ui.box_manage_choose_representation.currentIndex() == 1: 3058 cmd.show("cartoon", tmp_selection) 3059 cmd.hide("ribbon", tmp_selection) 3060 elif self._view.ui.box_manage_choose_representation.currentIndex() == 2: 3061 cmd.show("ribbon", tmp_selection) 3062 cmd.hide("cartoon", tmp_selection) 3063 else: 3064 print("Missing implementation!") 3065 3066 def choose_manage_bg_color(self) -> None: 3067 """Sets the background color.""" 3068 if self._view.ui.box_manage_choose_bg_color.currentIndex() == 0: 3069 print("Please select a background color.") 3070 self._view.status_bar.showMessage("Please select a background color.") 3071 elif self._view.ui.box_manage_choose_bg_color.currentIndex() == 1: 3072 cmd.bg_color("black") 3073 elif self._view.ui.box_manage_choose_bg_color.currentIndex() == 2: 3074 cmd.bg_color("white") 3075 else: 3076 print("Missing implementation!") 3077 3078 def show_disulfid_bonds_as_sticks(self) -> None: 3079 """Shows all disulfid bonds within the pymol session.""" 3080 tmp_pymol_selection_option: str = "byres (resn CYS and name SG) within 2 of (resn CYS and name SG)" 3081 cmd.select( 3082 name="disulfides", 3083 selection=f"{self._view.ui.box_manage_choose_protein.currentText()} & {tmp_pymol_selection_option}", 3084 ) 3085 cmd.color(color="atomic", selection="disulfides and not elem C") 3086 cmd.set("valence", 0) # this needs to be better implemented 3087 cmd.show("sticks", "disulfides") 3088 cmd.hide("sticks", "elem H") 3089 3090 def hide_disulfid_bonds_as_sticks(self) -> None: 3091 """Hides all disulfid bonds within the pymol session.""" 3092 tmp_pymol_selection_option: str = "byres (resn CYS and name SG) within 2 of (resn CYS and name SG)" 3093 cmd.select( 3094 name="disulfides", 3095 selection=f"{self._view.ui.box_manage_choose_protein.currentText()} & {tmp_pymol_selection_option}", 3096 ) 3097 cmd.hide("sticks", "disulfides") 3098 3099 # </editor-fold> 3100 3101 # <editor-fold desc="Image page functions"> 3102 def show_representation(self) -> None: 3103 """Sets the representation.""" 3104 if self._view.ui.box_representation.currentIndex() == 0: 3105 self.main_window_state.image_page.representation = "" 3106 self._view.status_bar.showMessage("Please select a representation.") 3107 elif self._view.ui.box_representation.currentIndex() == 1: 3108 cmd.show("cartoon", "all") 3109 cmd.hide("ribbon", "all") 3110 self.main_window_state.image_page.representation = "cartoon" 3111 elif self._view.ui.box_representation.currentIndex() == 2: 3112 cmd.show("ribbon", "all") 3113 cmd.hide("cartoon", "all") 3114 self.main_window_state.image_page.representation = "ribbon" 3115 else: 3116 print("Missing implementation!") 3117 3118 def choose_bg_color(self) -> None: 3119 """Sets the background color.""" 3120 if self._view.ui.box_bg_color.currentIndex() == 0: 3121 self.main_window_state.image_page.background_color = "" 3122 self._view.status_bar.showMessage("Please select a background color.") 3123 elif self._view.ui.box_bg_color.currentIndex() == 1: 3124 cmd.bg_color("black") 3125 self.main_window_state.image_page.background_color = "black" 3126 elif self._view.ui.box_bg_color.currentIndex() == 2: 3127 cmd.bg_color("white") 3128 self.main_window_state.image_page.background_color = "white" 3129 else: 3130 print("Missing implementation!") 3131 3132 def choose_renderer(self) -> None: 3133 """Sets the renderer.""" 3134 if self._view.ui.box_renderer.currentIndex() == 0: 3135 self._view.status_bar.showMessage("Please select a renderer.") 3136 self._view.ui.cb_ray_tracing.hide() 3137 self._view.ui.label_26.hide() 3138 elif self._view.ui.box_renderer.currentIndex() == 1: 3139 self.renderer = "-1" 3140 self._view.ui.cb_ray_tracing.show() 3141 self._view.ui.label_26.show() 3142 elif self._view.ui.box_renderer.currentIndex() == 2: 3143 self.renderer = "0" 3144 self._view.ui.cb_ray_tracing.show() 3145 self._view.ui.label_26.show() 3146 else: 3147 print("Missing implementation!") 3148 self.main_window_state.image_page.renderer = self._view.ui.box_renderer.currentIndex() 3149 3150 def choose_ray_trace_mode(self) -> None: 3151 """Sets the ray-trace mode.""" 3152 if self._view.ui.box_ray_trace_mode.currentIndex() == 0: 3153 self._view.status_bar.showMessage("Please select a Ray-Trace-Mode.") 3154 elif self._view.ui.box_ray_trace_mode.currentIndex() == 1: 3155 cmd.set("ray_trace_mode", 0) 3156 elif self._view.ui.box_ray_trace_mode.currentIndex() == 2: 3157 cmd.set("ray_trace_mode", 1) 3158 elif self._view.ui.box_ray_trace_mode.currentIndex() == 3: 3159 cmd.set("ray_trace_mode", 2) 3160 elif self._view.ui.box_ray_trace_mode.currentIndex() == 4: 3161 cmd.set("ray_trace_mode", 3) 3162 else: 3163 print("Missing implementation!") 3164 self.main_window_state.image_page.ray_trace_mode = self._view.ui.box_ray_trace_mode.currentIndex() 3165 3166 def choose_ray_texture(self) -> None: 3167 """Sets the ray texture.""" 3168 if self._view.ui.box_ray_texture.currentIndex() == 0: 3169 print("Please select a Ray Texture.") 3170 self._view.status_bar.showMessage("Please select a Ray Texture.") 3171 elif self._view.ui.box_ray_texture.currentIndex() == 1: 3172 cmd.set("ray_texture", 0) 3173 elif self._view.ui.box_ray_texture.currentIndex() == 2: 3174 cmd.set("ray_texture", 1) 3175 elif self._view.ui.box_ray_texture.currentIndex() == 3: 3176 cmd.set("ray_texture", 2) 3177 elif self._view.ui.box_ray_texture.currentIndex() == 4: 3178 cmd.set("ray_texture", 3) 3179 elif self._view.ui.box_ray_texture.currentIndex() == 5: 3180 cmd.set("ray_texture", 4) 3181 elif self._view.ui.box_ray_texture.currentIndex() == 6: 3182 cmd.set("ray_texture", 5) 3183 else: 3184 print("Missing implementation!") 3185 self.main_window_state.image_page.ray_texture = self._view.ui.box_ray_texture.currentIndex() 3186 3187 def decide_ray_tracing(self) -> None: 3188 """Sets the ray-tracing options.""" 3189 print(self._view.ui.cb_ray_tracing.isChecked()) 3190 if self._view.ui.cb_ray_tracing.isChecked(): 3191 self._view.ui.cb_transparent_bg.hide() 3192 self._view.ui.label_23.hide() 3193 self._view.ui.box_renderer.setEnabled(False) 3194 self._view.ui.label_10.show() 3195 self._view.ui.box_ray_trace_mode.show() 3196 self._view.ui.label_14.show() 3197 self._view.ui.box_ray_texture.show() 3198 cmd.set("ray_opaque_background", "off") 3199 else: 3200 self._view.ui.cb_transparent_bg.show() 3201 self._view.ui.label_23.show() 3202 self._view.ui.box_renderer.setEnabled(True) 3203 self._view.ui.label_10.hide() 3204 self._view.ui.box_ray_trace_mode.hide() 3205 self._view.ui.label_14.hide() 3206 self._view.ui.box_ray_texture.hide() 3207 self.main_window_state.image_page.ray_tracing = self._view.ui.cb_ray_tracing.isChecked() 3208 3209 def decide_transparent_bg(self) -> None: 3210 """Sets the transparent background.""" 3211 if self._view.ui.cb_transparent_bg.isChecked(): 3212 cmd.set("opaque_background", "off") 3213 else: 3214 cmd.set("opaque_background", "on") 3215 self.main_window_state.image_page.transparent_background = self._view.ui.cb_transparent_bg.isChecked() 3216 3217 @staticmethod 3218 def update_scene() -> None: 3219 """Updates the current selected PyMOL scene.""" 3220 cmd.scene(key="auto", action="update") 3221 3222 def save_scene(self) -> None: 3223 """Saves the current view as a new PyMOL scene.""" 3224 # returns tuple with (name, bool) 3225 scene_name = QtWidgets.QInputDialog.getText(self._view, "Save Scene", "Enter scene name:") 3226 if scene_name[1]: 3227 cmd.scene(key=scene_name[0], action="append") 3228 3229 def post_preview_image(self) -> None: 3230 """Hides the block box of the preview process.""" 3231 self.block_box_uni.hide() 3232 self.block_box_uni.destroy(True) 3233 self._view.status_bar.showMessage("Finished preview of ray-traced image.") 3234 QtWidgets.QApplication.restoreOverrideCursor() 3235 3236 def preview_image(self) -> None: 3237 """Previews the image.""" 3238 QtWidgets.QApplication.setOverrideCursor(Qt.WaitCursor) 3239 if self._view.ui.cb_ray_tracing.isChecked(): 3240 self._view.status_bar.showMessage("Preview ray-traced image ...") 3241 # <editor-fold desc="Worker setup"> 3242 # --Begin: worker setup 3243 self.tmp_thread = QtCore.QThread() 3244 self.tmp_worker = task_workers.PreviewRayImageWorker(self.renderer) 3245 self.tmp_thread = task_workers.setup_worker_for_work( 3246 self.tmp_thread, 3247 self.tmp_worker, 3248 self.display_view_page, 3249 ) 3250 self.tmp_worker.finished.connect(self.post_preview_image) 3251 self.tmp_thread.start() 3252 # --End: worker setup 3253 3254 # </editor-fold> 3255 gui_utils.setup_standard_block_box( 3256 self.block_box_uni, 3257 "Preview ray-trace image", 3258 "Creating preview for the ray-traced image ...", 3259 ) 3260 self.block_box_uni.exec_() 3261 else: 3262 self._view.status_bar.showMessage("Preview draw image ...") 3263 cmd.draw(2400, 2400) 3264 self._view.status_bar.showMessage("Finished preview of drawn image.") 3265 QtWidgets.QApplication.restoreOverrideCursor() 3266 3267 def post_save_image(self) -> None: 3268 """Displays a message box which informs that the process has finished.""" 3269 self.block_box_uni.hide() 3270 self.block_box_uni.destroy(True) 3271 self._view.status_bar.showMessage("Finished image creation.") 3272 QtWidgets.QApplication.restoreOverrideCursor() 3273 basic_boxes.ok("Finished image creation", "The image has been created.", QtWidgets.QMessageBox.Information) 3274 3275 def save_image(self) -> None: 3276 """Saves the image as a png file.""" 3277 QtWidgets.QApplication.setOverrideCursor(Qt.WaitCursor) 3278 if self._view.ui.cb_ray_tracing.isChecked(): 3279 save_dialog = QtWidgets.QFileDialog() 3280 try: 3281 full_file_name = save_dialog.getSaveFileName(caption="Save Image", filter="Image (*.png)") 3282 if full_file_name == ("", ""): 3283 tools.quick_log_and_display( 3284 "info", 3285 "No file has been selected.", 3286 self._view.status_bar, 3287 "No file has been selected.", 3288 ) 3289 return 3290 self._view.status_bar.showMessage("Creating ray-traced image ...") 3291 3292 # <editor-fold desc="Worker setup"> 3293 # --Begin: worker setup 3294 self.tmp_thread = QtCore.QThread() 3295 self.tmp_worker = task_workers.SaveRayImageWorker(self.renderer, full_file_name[0]) 3296 self.tmp_thread = task_workers.setup_worker_for_work( 3297 self.tmp_thread, 3298 self.tmp_worker, 3299 self.display_view_page, 3300 ) 3301 self.tmp_worker.finished.connect(self.post_save_image) 3302 self.tmp_thread.start() 3303 # --End: worker setup 3304 3305 # </editor-fold> 3306 gui_utils.setup_standard_block_box( 3307 self.block_box_uni, 3308 "Save ray-trace image", 3309 "Creating the ray-traced image ...", 3310 ) 3311 self.block_box_uni.exec_() 3312 3313 # cmd.ray(2400, 2400, renderer=int(self.renderer)) 3314 # cmd.png(full_file_name[0], dpi=300) 3315 3316 except FileExistsError: 3317 tools.quick_log_and_display( 3318 "error", 3319 "File exists already.", 3320 self._view.status_bar, 3321 "File exists already.", 3322 ) 3323 except pymol.CmdException: 3324 tools.quick_log_and_display( 3325 "error", 3326 "Unexpected Error from PyMOL while saving the " "an image", 3327 self._view.status_bar, 3328 "Unexpected Error from PyMOL", 3329 ) 3330 else: 3331 save_dialog = QtWidgets.QFileDialog() 3332 try: 3333 full_file_name = save_dialog.getSaveFileName(caption="Save Image", filter="Image (*.png)") 3334 if full_file_name == ("", ""): 3335 tools.quick_log_and_display( 3336 "info", 3337 "No file has been selected.", 3338 self._view.status_bar, 3339 "No file has been selected.", 3340 ) 3341 return 3342 self._view.status_bar.showMessage("Creating draw image ...") 3343 cmd.draw(2400, 2400) 3344 cmd.png(full_file_name[0], dpi=300) 3345 self._view.status_bar.showMessage("Finished image creation.") 3346 basic_boxes.ok( 3347 "Finished image creation", 3348 "The image has been created.", 3349 QtWidgets.QMessageBox.Information, 3350 ) 3351 except FileExistsError: 3352 tools.quick_log_and_display( 3353 "error", 3354 "File exists already.", 3355 self._view.status_bar, 3356 "File exists already.", 3357 ) 3358 except pymol.CmdException: 3359 tools.quick_log_and_display( 3360 "error", 3361 "Unexpected Error from PyMOL while saving the " "an image", 3362 self._view.status_bar, 3363 "Unexpected Error from PyMOL", 3364 ) 3365 finally: 3366 QtWidgets.QApplication.restoreOverrideCursor() 3367 3368 # </editor-fold> 3369 3370 # <editor-fold desc="Hotspots page functions"> 3371 def open_protein_for_hotspots(self) -> None: 3372 """Loads the selected protein's pymol session.""" 3373 self._view.wait_spinner.start() 3374 try: 3375 tmp_name = self._view.ui.list_hotspots_choose_protein.currentItem().text() 3376 except AttributeError: 3377 self._view.wait_spinner.stop() 3378 return 3379 if self._view.ui.list_hotspots_choose_protein.currentItem().text() != "": 3380 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 3381 self._active_task = tasks.Task( 3382 target=main_presenter_async.open_protein_for_hotspots, 3383 args=( 3384 tmp_name, 3385 self._current_project, 3386 self.current_session, 3387 ), 3388 post_func=self.__await_open_protein_for_hotspots, 3389 ) 3390 self._active_task.start() 3391 self.update_status("Loading PyMOL session ...") 3392 else: 3393 self._view.wait_spinner.stop() 3394 self.update_status(self._workspace_status) 3395 3396 def __await_open_protein_for_hotspots(self, result: tuple) -> None: 3397 _, is_protein, is_protein_pair, self.current_session = result 3398 if is_protein and not is_protein_pair: 3399 gui_elements_to_show = [ 3400 self._view.ui.lbl_hotspots_resi_show, 3401 self._view.ui.btn_hotspots_resi_show, 3402 self._view.ui.lbl_hotspots_resi_hide, 3403 self._view.ui.btn_hotspots_resi_hide, 3404 self._view.ui.lbl_hotspots_resi_zoom, 3405 self._view.ui.btn_hotspots_resi_zoom, 3406 self._view.ui.btn_manage_session, 3407 ] 3408 gui_utils.show_gui_elements(gui_elements_to_show) 3409 elif is_protein_pair and not is_protein: 3410 gui_elements_to_show = [ 3411 self._view.ui.lbl_hotspots_resi_show, 3412 self._view.ui.btn_hotspots_resi_show, 3413 self._view.ui.lbl_hotspots_resi_hide, 3414 self._view.ui.btn_hotspots_resi_hide, 3415 self._view.ui.lbl_hotspots_resi_zoom, 3416 self._view.ui.btn_hotspots_resi_zoom, 3417 self._view.ui.btn_manage_session, 3418 ] 3419 gui_utils.show_gui_elements(gui_elements_to_show) 3420 else: 3421 pass 3422 self._view.wait_spinner.stop() 3423 self.update_status(self._workspace_status) 3424 3425 @staticmethod 3426 def hide_resi_sticks() -> None: 3427 """Hides the balls and sticks representation of the pymol selection.""" 3428 session_util.check_if_sele_is_empty() 3429 cmd.hide(representation="sticks", selection="sele") 3430 3431 @staticmethod 3432 def show_resi_sticks() -> None: 3433 """Shows the pymol selection as sticks.""" 3434 session_util.check_if_sele_is_empty() 3435 cmd.show(representation="sticks", selection="sele and not hydrogens") 3436 cmd.select(name="sele", selection="sele and not hydrogens") 3437 cmd.color(color="atomic", selection="sele and not elem C") 3438 cmd.set("valence", 0) # this needs to be better implemented 3439 3440 @staticmethod 3441 def zoom_resi_position() -> None: 3442 """Zooms to the pymol selection.""" 3443 session_util.check_if_sele_is_empty() 3444 cmd.zoom(selection="sele", buffer=8.0, state=0, complete=0) 3445 3446 # </editor-fold> 3447 3448 # </editor-fold> 3449 3450 # <editor-fold desc="GUI related methods"> 3451 3452 # <editor-fold desc="GUI page management functions"> 3453 def _create_batch_analysis_management(self) -> None: 3454 """Creates a list of gui stages.""" 3455 # gui element management 3456 tmp_stages = [ 3457 # add a prot analysis: stage 0 3458 stage.Stage( 3459 { 3460 "label_batch_analysis_overview": self._view.ui.lbl_analysis_batch_overview, 3461 "box_protein_structure_1": self._view.ui.list_analysis_batch_overview, 3462 }, 3463 { 3464 "add_button": self._view.ui.btn_analysis_batch_add, 3465 "remove_button": self._view.ui.btn_analysis_batch_remove, 3466 }, 3467 ), 3468 # choose protein structures: stage 1 3469 stage.Stage( 3470 { 3471 "label_protein_structure_1": self._view.ui.lbl_analysis_batch_prot_struct_1, 3472 "box_protein_structure_1": self._view.ui.box_analysis_batch_prot_struct_1, 3473 "label_vs": self._view.ui.lbl_analysis_batch_vs, 3474 "label_protein_structure_2": self._view.ui.lbl_analysis_batch_prot_struct_2, 3475 "box_protein_structure_2": self._view.ui.box_analysis_batch_prot_struct_2, 3476 }, 3477 { 3478 "next_button": self._view.ui.btn_analysis_batch_next, 3479 "back_button": self._view.ui.btn_analysis_batch_back, 3480 }, 3481 ), 3482 # choose chains from prot structure 1: stage 2 3483 stage.Stage( 3484 { 3485 "label_protein_structure_1_chains": self._view.ui.lbl_analysis_batch_ref_chains, 3486 "list_protein_structure_1_chains": self._view.ui.list_analysis_batch_ref_chains, 3487 }, 3488 { 3489 "back_button": self._view.ui.btn_analysis_batch_back_2, 3490 "next_button": self._view.ui.btn_analysis_batch_next_2, 3491 }, 3492 ), 3493 # choose chains from prot structure 2: stage 3 3494 stage.Stage( 3495 { 3496 "label_protein_structure_2_chains": self._view.ui.lbl_analysis_batch_model_chains, 3497 "list_protein_structure_2_chains": self._view.ui.list_analysis_batch_model_chains, 3498 }, 3499 { 3500 "back_button": self._view.ui.btn_analysis_batch_back_3, 3501 "next_button": self._view.ui.btn_analysis_batch_next_3, 3502 }, 3503 ), 3504 # start batch run: stage 4 3505 stage.Stage( 3506 { 3507 "label_images": self._view.ui.lbl_analysis_batch_images, 3508 "checkbox_images": self._view.ui.cb_analysis_batch_images, 3509 }, 3510 { 3511 "start_button": self._view.ui.btn_analysis_batch_start, 3512 }, 3513 ), 3514 ] 3515 self.batch_analysis_management = gui_page_management.GuiPageManagement(tmp_stages) 3516 3517 def _create_results_management(self) -> None: 3518 """Creates a list of gui stages.""" 3519 # gui element management 3520 tmp_stages = [ 3521 # choose protein structures: stage 0 3522 stage.Stage( 3523 { 3524 "label_analysis_options": self._view.ui.lbl_results_analysis_options, 3525 "box_results_analysis_options": self._view.ui.cb_results_analysis_options, 3526 }, 3527 { 3528 "": None, 3529 }, 3530 ), 3531 # choose chains from prot structure 1: stage 1 3532 stage.Stage( 3533 { 3534 "label_results_rmsd": self._view.ui.lbl_results_rmsd, 3535 "text_results_rmsd": self._view.ui.txt_results_rmsd, 3536 "label_color_rmsd": self._view.ui.lbl_color_rmsd, 3537 "button_color_rmsd": self._view.ui.btn_color_rmsd, 3538 "label_results_aligned_residues": self._view.ui.lbl_results_aligned_residues, 3539 "text_results_aligned_residues": self._view.ui.txt_results_aligned_residues, 3540 "label_results_distance_plot": self._view.ui.lbl_results_distance_plot, 3541 "button_view_distance_plot": self._view.ui.btn_view_distance_plot, 3542 "label_results_distance_histogram": self._view.ui.lbl_results_distance_histogram, 3543 "button_view_distance_histogram": self._view.ui.btn_view_distance_histogram, 3544 "label_results_distance_table": self._view.ui.lbl_results_distance_table, 3545 "button_view_distance_table": self._view.ui.btn_view_distance_table, 3546 "label_results_structure_alignment": self._view.ui.lbl_results_structure_alignment, 3547 "button_view_struct_alignment": self._view.ui.btn_view_struct_alignment, 3548 "label_results_interest_regions": self._view.ui.lbl_results_interest_regions, 3549 "list_results_interest_regions": self._view.ui.list_results_interest_regions, 3550 "button_results_interest_regions": self._view.ui.btn_view_interesting_region, 3551 }, 3552 { 3553 "": None, 3554 }, 3555 ), 3556 ] 3557 self.results_management = gui_page_management.GuiPageManagement(tmp_stages) 3558 3559 # </editor-fold> 3560 3561 # <editor-fold desc="Page init functions"> 3562 def _init_fill_combo_boxes(self) -> None: 3563 """Fills all combo boxes of the plugin.""" 3564 item_list_representation = [ 3565 "", 3566 "cartoon", 3567 "ribbon", 3568 ] 3569 gui_utils.fill_combo_box(self._view.ui.box_representation, item_list_representation) 3570 gui_utils.fill_combo_box(self._view.ui.box_manage_choose_representation, item_list_representation) 3571 # combo box BgColor 3572 item_list_bg_color = [ 3573 "", 3574 "black", 3575 "white", 3576 ] 3577 gui_utils.fill_combo_box(self._view.ui.box_bg_color, item_list_bg_color) 3578 gui_utils.fill_combo_box(self._view.ui.box_manage_choose_bg_color, item_list_bg_color) 3579 # combo box Renderer 3580 item_list_renderer = [ 3581 "", 3582 "default renderer", 3583 "PyMOL internal renderer", 3584 ] 3585 gui_utils.fill_combo_box(self._view.ui.box_renderer, item_list_renderer) 3586 # combo box RayTraceMode 3587 item_list_ray_trace_mode = [ 3588 "", 3589 "normal color", 3590 "normal color + black outline", 3591 "black outline only", 3592 "quantized color + black outline", 3593 ] 3594 gui_utils.fill_combo_box(self._view.ui.box_ray_trace_mode, item_list_ray_trace_mode) 3595 # combo box Ray Texture 3596 item_list_ray_texture = [ 3597 "", 3598 "None", 3599 "Matte 1", 3600 "Matte 2", 3601 "Swirl 1", 3602 "Fiber", 3603 ] 3604 gui_utils.fill_combo_box(self._view.ui.box_ray_texture, item_list_ray_texture) 3605 # combo box protein Colors 3606 gui_utils.fill_combo_box(self._view.ui.box_manage_choose_color, constants.PYMOL_COLORS) 3607 3608 def _init_new_page(self) -> None: 3609 """Clears all text fields and hides everything which is needed.""" 3610 self._view.ui.txt_new_project_name.clear() 3611 self._view.ui.txt_new_choose_reference.clear() 3612 self._view.ui.lbl_new_status_project_name.setText("") 3613 self._view.ui.lbl_new_status_choose_reference.setText("") 3614 self._view.ui.cb_new_add_reference.setCheckState(0) 3615 self._view.ui.btn_new_create_project.setEnabled(False) 3616 styles.color_button_not_ready(self._view.ui.btn_new_create_project) 3617 3618 def _init_use_page(self) -> None: 3619 """Clears all text fields and hides everything which is needed.""" 3620 gui_elements = [ 3621 self._view.ui.lbl_use_search, 3622 self._view.ui.lbl_use_status_search, 3623 self._view.ui.txt_use_search, 3624 self._view.ui.btn_use_add_available_protein_structures, 3625 self._view.ui.lbl_use_available_protein_structures, 3626 self._view.ui.list_use_available_protein_structures, 3627 self._view.ui.btn_use_remove_selected_protein_structures, 3628 self._view.ui.lbl_use_selected_protein_structures, 3629 self._view.ui.list_use_selected_protein_structures, 3630 self._view.ui.btn_use_back, 3631 self._view.ui.btn_use_create_new_project, 3632 self._view.ui.lbl_use_new_project, 3633 ] 3634 gui_utils.hide_gui_elements(gui_elements) 3635 self._view.ui.txt_use_project_name.clear() 3636 self._view.ui.lbl_use_status_project_name.setText("") 3637 self._view.ui.txt_use_search.clear() 3638 self._view.ui.lbl_use_status_search.setText("") 3639 self._view.ui.list_use_available_protein_structures.clear() 3640 self._view.ui.list_use_selected_protein_structures.clear() 3641 self._view.ui.list_use_existing_projects.clear() 3642 self._view.ui.btn_use_next.setEnabled(False) 3643 self.hide_protein_selection_for_use() 3644 3645 def _init_edit_page(self) -> None: 3646 """Clears all text fields and hides everything which is needed.""" 3647 self._view.ui.list_edit_project_proteins.clear() 3648 gui_elements_to_hide = [ 3649 self._view.ui.lbl_edit_clean_new_prot, 3650 self._view.ui.btn_edit_clean_new_prot, 3651 self._view.ui.lbl_edit_clean_update_prot, 3652 self._view.ui.btn_edit_clean_update_prot, 3653 self._view.ui.label_12, 3654 self._view.ui.btn_edit_project_delete, 3655 self._view.ui.label_15, 3656 self._view.ui.btn_edit_protein_rename, 3657 self._view.ui.btn_edit_project_save, 3658 self._view.ui.label_13, 3659 ] 3660 gui_utils.hide_gui_elements(gui_elements_to_hide) 3661 gui_utils.fill_list_view_with_protein_names(self._current_project, self._view.ui.list_edit_project_proteins) 3662 # self.project_scanner.scan_project_for_valid_proteins(self._view.ui.list_edit_project_proteins) 3663 3664 def _init_sequence_vs_pdb_page(self) -> None: 3665 """Clears all text fields and hides everything which is needed.""" 3666 self._view.ui.list_s_v_p_ref_chains.clear() 3667 # # sets up defaults: Prediction + Analysis 3668 # 3669 # #self._view.ui.label_18.hide() 3670 # #self._view.ui.txt_prediction_project_name.hide() 3671 # #self._view.ui.lbl_prediction_status_project_name.hide() 3672 # # stage 1 3673 # self._view.ui.lbl_prediction_status_project_name.setText("") 3674 # 3675 # #self._view.ui.list_widget_projects.hide() 3676 # #self._view.ui.btn_prediction_next_1.hide() 3677 # # stage 2 3678 # self._view.ui.lbl_prediction_load_reference.hide() 3679 # self._view.ui.txt_prediction_load_reference.clear() 3680 # self._view.ui.txt_prediction_load_reference.hide() 3681 # self._view.ui.lbl_prediction_status_load_reference.setText("") 3682 # self._view.ui.btn_prediction_back_2.setEnabled(False) 3683 # self._view.ui.btn_prediction_back_2.hide() 3684 # self._view.ui.btn_prediction_next_2.setEnabled(False) 3685 # self._view.ui.btn_prediction_next_2.hide() 3686 # 3687 # # stage 3 3688 # self._view.ui.lbl_prediction_ref_chains.hide() 3689 # self._view.ui.list_widget_ref_chains.hide() 3690 # # TO-DO: stylesheet needs to be integrated into the styles.css 3691 # self._view.ui.list_widget_ref_chains.setStyleSheet("border-style: solid;" 3692 # "border-width: 2px;" 3693 # "border-radius: 8px;" 3694 # "border-color: #DCDBE3;") 3695 # self._view.ui.list_widget_ref_chains.setSelectionMode(PyQt5.QtWidgets.QAbstractItemView.ExtendedSelection) 3696 # self._view.ui.btn_prediction_back_3.setEnabled(False) 3697 # self._view.ui.btn_prediction_back_3.hide() 3698 # self._view.ui.btn_prediction_start.setEnabled(False) 3699 # self._view.ui.btn_prediction_start.hide() 3700 # # TO-DO: needs to be removed if model chains are implemented at the right spot 3701 # self._view.ui.lbl_prediction_model_chains.hide() 3702 # self._view.ui.txt_prediction_chain_model.hide() 3703 3704 def _init_results_page(self) -> None: 3705 """Clears all text fields and hides everything which is needed.""" 3706 # stage 1 3707 self._view.ui.list_results_interest_regions.clear() 3708 self._view.ui.txt_results_rmsd.clear() 3709 self._view.ui.txt_results_aligned_residues.clear() 3710 3711 def _init_analysis_image_page(self) -> None: 3712 """Clears all text fields and hides everything which is needed.""" 3713 self._view.ui.list_analysis_images_struct_analysis.setEnabled(True) 3714 self._view.ui.list_analysis_images_creation_struct_analysis.setEnabled(True) 3715 self.display_image_analysis_page() 3716 3717 def _init_image_page(self) -> None: 3718 """Hides everything which is needed.""" 3719 self._view.ui.label_10.hide() 3720 self._view.ui.box_ray_trace_mode.hide() 3721 self._view.ui.label_14.hide() 3722 self._view.ui.box_ray_texture.hide() 3723 3724 def _init_batch_analysis_page(self) -> None: 3725 """Clears all text fields and hides everything which is needed.""" 3726 # sets up defaults: Batch 3727 self.batch_analysis_management.show_stage_x(0) 3728 self._view.ui.list_analysis_batch_overview.clear() 3729 self._view.ui.btn_analysis_batch_remove.hide() 3730 3731 def _init_all_pages(self) -> None: 3732 """Collection of all init methods to reset all page defaults.""" 3733 self._init_local_pred_mono_page() 3734 self._init_local_pred_multi_page() 3735 self._init_mono_pred_analysis_page() 3736 self._init_multi_pred_analysis_page() 3737 self._init_sequence_vs_pdb_page() 3738 self._init_batch_analysis_page() 3739 self._init_analysis_image_page() 3740 self._init_results_page() 3741 self._init_image_page() 3742 3743 # </editor-fold> 3744 3745 # <editor-fold desc="Display page functions"> 3746 def display_home_page(self) -> None: 3747 """Displays the homepage of the plugin.""" 3748 if self.is_distance_plot_open: 3749 self.distance_plot_dialog.close() 3750 self.is_distance_plot_open = False 3751 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 0, "Home") 3752 3753 def display_job_analysis_page(self) -> None: 3754 """Displays the job analysis work area.""" 3755 self._view.ui.list_analysis_batch_ref_chains.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection) 3756 self._view.ui.list_analysis_batch_model_chains.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection) 3757 # regular work area opening 3758 self._init_batch_analysis_page() 3759 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 4, "Structure Analysis") 3760 self.last_sidebar_button = styles.color_sidebar_buttons( 3761 self.last_sidebar_button, 3762 self._view.ui.btn_batch_analysis_page, 3763 ) 3764 3765 def display_results_page(self) -> None: 3766 """Displays the results work area.""" 3767 if self.is_distance_plot_open: 3768 self.distance_plot_dialog.close() 3769 self.is_distance_plot_open = False 3770 results = [] 3771 results.insert(0, "") 3772 3773 for tmp_protein_pair in self._current_project.protein_pairs: 3774 results.append(tmp_protein_pair.name) 3775 if tmp_protein_pair.name == self.results_name: 3776 pass 3777 self._view.ui.cb_results_analysis_options.clear() 3778 gui_utils.fill_combo_box(self._view.ui.cb_results_analysis_options, results) 3779 3780 desired_string: str = self.main_window_state.results_page.results_name 3781 # Find the index of the string in the combo box 3782 index = self._view.ui.cb_results_analysis_options.findText(desired_string) 3783 # Set the current index of the combo box 3784 if index != -1: 3785 self._view.ui.cb_results_analysis_options.setCurrentIndex(index) 3786 else: 3787 print(f"String '{desired_string}' not found in the combo box.") 3788 3789 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 5, "Results") 3790 self.last_sidebar_button = styles.color_sidebar_buttons( 3791 self.last_sidebar_button, 3792 self._view.ui.btn_results_page, 3793 ) 3794 3795 def display_image_page(self) -> None: 3796 """Displays the image work area.""" 3797 if self.is_distance_plot_open: 3798 self.distance_plot_dialog.close() 3799 self.is_distance_plot_open = False 3800 self._init_image_page() 3801 3802 if self.main_window_state.image_page.transparent_background: 3803 self._view.ui.cb_transparent_bg.setChecked(True) 3804 else: 3805 self._view.ui.cb_transparent_bg.setChecked(False) 3806 if self.main_window_state.image_page.ray_tracing: 3807 self._view.ui.cb_ray_tracing.setChecked(True) 3808 else: 3809 self._view.ui.cb_ray_tracing.setChecked(False) 3810 try: 3811 self._view.ui.box_representation.setCurrentIndex( 3812 self._view.ui.box_representation.findText(self.main_window_state.image_page.representation), 3813 ) 3814 self._view.ui.box_bg_color.setCurrentIndex( 3815 self._view.ui.box_bg_color.findText(self.main_window_state.image_page.background_color), 3816 ) 3817 self._view.ui.box_renderer.setCurrentIndex(self.main_window_state.image_page.renderer) 3818 self._view.ui.box_ray_trace_mode.setCurrentIndex(self.main_window_state.image_page.ray_trace_mode) 3819 self._view.ui.box_ray_texture.setCurrentIndex(self.main_window_state.image_page.ray_texture) 3820 except IndexError: 3821 constants.PYSSA_LOGGER.error("An option is invalid.") 3822 3823 if self._view.ui.box_renderer.currentText() == "": 3824 self._view.ui.cb_ray_tracing.hide() 3825 self._view.ui.label_26.hide() 3826 else: 3827 self._view.ui.cb_ray_tracing.show() 3828 self._view.ui.label_26.show() 3829 3830 if self._view.ui.cb_ray_tracing.isChecked(): 3831 self._view.ui.label_10.show() 3832 self._view.ui.box_ray_trace_mode.show() 3833 self._view.ui.label_14.show() 3834 self._view.ui.box_ray_texture.show() 3835 else: 3836 self._view.ui.label_10.hide() 3837 self._view.ui.box_ray_trace_mode.hide() 3838 self._view.ui.label_14.hide() 3839 self._view.ui.box_ray_texture.hide() 3840 3841 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_image_page) 3842 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 6, "Image") 3843 3844 def display_new_page(self) -> None: 3845 """Displays the new project work area.""" 3846 self._init_new_page() 3847 self._view.ui.list_new_projects.clear() 3848 # pre-process 3849 gui_elements_to_hide = [ 3850 self._view.ui.lbl_new_choose_reference, 3851 self._view.ui.txt_new_choose_reference, 3852 self._view.ui.btn_new_choose_reference, 3853 ] 3854 gui_utils.hide_gui_elements(gui_elements_to_hide) 3855 self._view.status_bar.showMessage(self._workspace_label.text()) 3856 tools.scan_workspace_for_valid_projects(self._workspace_path, self._view.ui.list_new_projects) 3857 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 7, "Create new project") 3858 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_new_page) 3859 3860 def display_open_page(self) -> None: 3861 """Displays the open project work area.""" 3862 self._view.ui.txt_open_search.clear() 3863 self._view.ui.txt_open_selected_project.clear() 3864 if safeguard.Safeguard.check_filepath(self._workspace_path): 3865 self._view.ui.list_open_projects.clear() 3866 # pre-process 3867 self._view.status_bar.showMessage(self._workspace_label.text()) 3868 try: 3869 tools.scan_workspace_for_valid_projects(self._workspace_path, self._view.ui.list_open_projects) 3870 except PermissionError: 3871 gui_utils.error_dialog_settings( 3872 "The settings file is corrupted. Please restore the settings!", 3873 "", 3874 self._application_settings, 3875 ) 3876 self.display_home_page() 3877 return 3878 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 8, "Open existing project") 3879 self.last_sidebar_button = styles.color_sidebar_buttons( 3880 self.last_sidebar_button, 3881 self._view.ui.btn_open_page, 3882 ) 3883 else: 3884 gui_utils.error_dialog_settings( 3885 "The settings file is corrupted. Please restore the settings!", 3886 "", 3887 self._application_settings, 3888 ) 3889 self.display_home_page() 3890 3891 def display_delete_page(self) -> None: 3892 """Displays the "delete" project work area.""" 3893 self._view.ui.txt_delete_search.clear() 3894 self._view.ui.txt_delete_selected_projects.clear() 3895 self._view.ui.list_delete_projects.clear() 3896 # pre-process 3897 self._view.status_bar.showMessage(self._workspace_label.text()) 3898 tools.scan_workspace_for_valid_projects(self._workspace_path, self._view.ui.list_delete_projects) 3899 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 9, "Delete existing project") 3900 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_delete_page) 3901 3902 def display_edit_page(self) -> None: 3903 """Displays the edit project page.""" 3904 if self.is_distance_plot_open: 3905 self.distance_plot_dialog.close() 3906 self.is_distance_plot_open = False 3907 # pre-process 3908 self._view.status_bar.showMessage(self._workspace_label.text()) 3909 self._init_edit_page() 3910 tools.switch_page( 3911 self._view.ui.stackedWidget, 3912 self._view.ui.lbl_page_title, 3913 13, 3914 "Edit proteins of current project", 3915 ) 3916 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_edit_page) 3917 if len(self._view.ui.list_edit_project_proteins) >= 2: 3918 self._view.ui.btn_edit_existing_protein_struct.hide() 3919 self._view.ui.lbl_edit_existing_protein_struct.hide() 3920 else: 3921 self._view.ui.btn_edit_existing_protein_struct.show() 3922 self._view.ui.lbl_edit_existing_protein_struct.show() 3923 3924 def display_hotspots_page(self) -> None: 3925 """Displays the hotspots page.""" 3926 if self.is_distance_plot_open: 3927 self.distance_plot_dialog.close() 3928 self.is_distance_plot_open = False 3929 try: 3930 print(self._view.ui.list_hotspots_choose_protein.currentItem().text()) 3931 except AttributeError: 3932 self._view.ui.list_hotspots_choose_protein.clear() 3933 gui_elements_to_hide = [ 3934 self._view.ui.lbl_hotspots_resi_no, 3935 self._view.ui.sp_hotspots_resi_no, 3936 self._view.ui.lbl_hotspots_resi_show, 3937 self._view.ui.btn_hotspots_resi_show, 3938 self._view.ui.lbl_hotspots_resi_hide, 3939 self._view.ui.btn_hotspots_resi_hide, 3940 self._view.ui.lbl_hotspots_resi_zoom, 3941 self._view.ui.btn_hotspots_resi_zoom, 3942 ] 3943 gui_utils.hide_gui_elements(gui_elements_to_hide) 3944 gui_utils.fill_list_view_with_protein_names( 3945 self._current_project, 3946 self._view.ui.list_hotspots_choose_protein, 3947 ) 3948 gui_utils.fill_list_view_with_protein_pair_names( 3949 self._current_project, 3950 self._view.ui.list_hotspots_choose_protein, 3951 ) 3952 # self.project_scanner.scan_project_for_valid_proteins(self._view.ui.list_hotspots_choose_protein) 3953 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 18, "Hotspots") 3954 self.last_sidebar_button = styles.color_sidebar_buttons( 3955 self.last_sidebar_button, 3956 self._view.ui.btn_hotspots_page, 3957 ) 3958 3959 def display_manage_pymol_session(self) -> None: 3960 """Displays the manage pymol session page.""" 3961 if self.is_distance_plot_open: 3962 self.distance_plot_dialog.close() 3963 self.is_distance_plot_open = False 3964 self._view.ui.box_manage_choose_protein.clear() 3965 pymol_objs = cmd.get_object_list() 3966 pymol_objs.insert(0, "") 3967 for tmp_object in pymol_objs: 3968 self._view.ui.box_manage_choose_protein.addItem(tmp_object) 3969 self._view.ui.box_manage_choose_protein.setCurrentIndex( 3970 self.pymol_session_specs[pyssa_keys.SESSION_SPEC_PROTEIN][0], 3971 ) 3972 self._view.ui.box_manage_choose_color.setCurrentIndex( 3973 self.pymol_session_specs[pyssa_keys.SESSION_SPEC_COLOR][0], 3974 ) 3975 self._view.ui.box_manage_choose_representation.setCurrentIndex( 3976 self.pymol_session_specs[pyssa_keys.SESSION_SPEC_REPRESENTATION][0], 3977 ) 3978 self._view.ui.box_manage_choose_bg_color.setCurrentIndex( 3979 self.pymol_session_specs[pyssa_keys.SESSION_SPEC_BG_COLOR][0], 3980 ) 3981 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 24, "Manage PyMOL session") 3982 self.last_sidebar_button = styles.color_sidebar_buttons( 3983 self.last_sidebar_button, 3984 self._view.ui.btn_manage_session, 3985 ) 3986 gui_elements_to_hide = [ 3987 self._view.ui.lbl_manage_choose_color, 3988 self._view.ui.box_manage_choose_color, 3989 self._view.ui.lbl_manage_choose_representation, 3990 self._view.ui.box_manage_choose_representation, 3991 self._view.ui.lbl_manage_choose_bg_color, 3992 self._view.ui.box_manage_choose_bg_color, 3993 self._view.ui.lbl_disulfid_bond_1, 3994 self._view.ui.lbl_disulfid_bond_2, 3995 self._view.ui.btn_disulfid_bond_show, 3996 self._view.ui.btn_disulfid_bond_hide, 3997 ] 3998 gui_utils.hide_gui_elements(gui_elements_to_hide) 3999 4000 # </editor-fold> 4001 4002 # <editor-fold desc="New project"> 4003 def show_add_reference(self) -> None: 4004 """Shows the reference input section.""" 4005 # checkbox is checked 4006 self._view.ui.cb_new_add_reference.checkState() 4007 if self._view.ui.cb_new_add_reference.checkState() == 2: 4008 self._view.ui.txt_new_choose_reference.clear() 4009 self._view.ui.txt_new_choose_reference.setStyleSheet("background-color: white") 4010 self._view.ui.lbl_new_choose_reference.show() 4011 self._view.ui.txt_new_choose_reference.show() 4012 self._view.ui.btn_new_choose_reference.show() 4013 self._view.ui.btn_new_create_project.setEnabled(False) 4014 styles.color_button_not_ready(self._view.ui.btn_new_create_project) 4015 # check internet connectivity 4016 if not tools.check_internet_connectivity(): 4017 gui_utils.no_internet_dialog() 4018 self._view.ui.txt_new_choose_reference.setEnabled(False) 4019 self._view.ui.lbl_new_status_choose_reference.setText("You cannot enter a PDB ID (no internet).") 4020 return 4021 self._view.ui.txt_new_choose_reference.setEnabled(True) 4022 self._view.ui.lbl_new_status_choose_reference.setText("") 4023 else: 4024 self._view.ui.lbl_new_choose_reference.hide() 4025 self._view.ui.txt_new_choose_reference.hide() 4026 self._view.ui.btn_new_choose_reference.hide() 4027 self._view.ui.lbl_new_status_choose_reference.setText("") 4028 self._view.ui.btn_new_create_project.setEnabled(True) 4029 4030 def load_reference_in_project(self) -> None: 4031 """Loads a reference in a new project.""" 4032 try: 4033 # open file dialog 4034 file_name = QtWidgets.QFileDialog.getOpenFileName( 4035 self._view, 4036 "Open Reference", 4037 QtCore.QDir.homePath(), 4038 "PDB Files (*.pdb)", 4039 ) 4040 if file_name == ("", ""): 4041 raise ValueError 4042 # display path in text box 4043 self._view.ui.txt_new_choose_reference.setText(str(file_name[0])) 4044 self._view.ui.txt_new_choose_reference.setEnabled(False) 4045 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #000000") 4046 self._view.ui.btn_new_create_project.setEnabled(True) 4047 except ValueError: 4048 print("No file has been selected.") 4049 4050 def validate_reference_in_project(self) -> None: 4051 """Checks if the entered reference protein is valid or not.""" 4052 if len(self._view.ui.txt_new_choose_reference.text()) == 0: 4053 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4054 self._view.ui.lbl_new_status_choose_reference.setText("") 4055 self._view.ui.btn_new_create_project.setEnabled(False) 4056 styles.color_button_not_ready(self._view.ui.btn_new_create_project) 4057 elif len(self._view.ui.txt_new_choose_reference.text()) < 4: 4058 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4059 styles.color_button_not_ready(self._view.ui.btn_new_create_project) 4060 self._view.ui.btn_new_create_project.setEnabled(False) 4061 self._view.ui.lbl_new_status_choose_reference.setText("") 4062 # checks if a pdb id was entered 4063 elif len(self._view.ui.txt_new_choose_reference.text()) == 4: 4064 pdb_id = self._view.ui.txt_new_choose_reference.text().upper() 4065 try: 4066 # the pdb file gets saved in a scratch directory where it gets deleted immediately 4067 cmd.fetch(pdb_id, type="pdb", path=constants.SCRATCH_DIR) 4068 os.remove(f"{constants.SCRATCH_DIR}/{pdb_id}.pdb") 4069 cmd.reinitialize() 4070 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #000000") 4071 self._view.ui.btn_new_create_project.setEnabled(True) 4072 # if the id does not exist an exception gets raised 4073 except pymol.CmdException: 4074 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4075 return 4076 except FileNotFoundError: 4077 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4078 self._view.ui.lbl_new_status_choose_reference.setText("Invalid PDB ID.") 4079 self._view.ui.btn_new_create_project.setEnabled(False) 4080 return 4081 else: 4082 if self._view.ui.txt_new_choose_reference.text().find("/") == -1: 4083 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4084 self._view.ui.btn_new_create_project.setEnabled(False) 4085 styles.color_button_not_ready(self._view.ui.btn_new_create_project) 4086 4087 elif self._view.ui.txt_new_choose_reference.text().find("\\") == -1: 4088 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4089 self._view.ui.btn_new_create_project.setEnabled(False) 4090 styles.color_button_not_ready(self._view.ui.btn_new_create_project) 4091 4092 def validate_project_name(self) -> None: 4093 """Validates the input of the project name in real-time.""" 4094 input_validator.InputValidator.validate_project_name( 4095 self._view.ui.list_new_projects, 4096 self._view.ui.txt_new_project_name, 4097 self._view.ui.lbl_new_status_project_name, 4098 self._view.ui.btn_new_create_project, 4099 self._view.ui.cb_new_add_reference, 4100 ) 4101 4102 # </editor-fold> 4103 4104 # <editor-fold desc="Open project"> 4105 def validate_open_search(self) -> None: 4106 """Validates the input of the project name in real-time.""" 4107 if self._view.ui.list_open_projects.currentItem() is not None: 4108 self._view.ui.list_open_projects.currentItem().setSelected(False) 4109 # set color for lineEdit 4110 input_validator.InputValidator.validate_search_input( 4111 self._view.ui.list_open_projects, 4112 self._view.ui.txt_open_search, 4113 self._view.ui.lbl_open_status_search, 4114 self._view.ui.txt_open_selected_project, 4115 ) 4116 4117 def select_project_from_open_list(self) -> None: 4118 """Sets the selected project name in the text box.""" 4119 try: 4120 self._view.ui.txt_open_selected_project.setText(self._view.ui.list_open_projects.currentItem().text()) 4121 except AttributeError: 4122 self._view.ui.txt_open_selected_project.setText("") 4123 4124 def activate_open_button(self) -> None: 4125 """Activates the open button.""" 4126 if self._view.ui.txt_open_selected_project.text() == "": 4127 self._view.ui.btn_open_open_project.setEnabled(False) 4128 else: 4129 self._view.ui.btn_open_open_project.setEnabled(True) 4130 4131 # </editor-fold> 4132 4133 # <editor-fold desc="Delete project"> 4134 def select_project_from_delete_list(self) -> None: 4135 """Selects a project from the project list on the delete page.""" 4136 try: 4137 self._view.ui.txt_delete_selected_projects.setText(self._view.ui.list_delete_projects.currentItem().text()) 4138 except AttributeError: 4139 self._view.ui.txt_delete_selected_projects.setText("") 4140 4141 def activate_delete_button(self) -> None: 4142 """Activates the delete button.""" 4143 if self._view.ui.txt_delete_selected_projects.text() == "": 4144 self._view.ui.btn_delete_delete_project.setEnabled(False) 4145 else: 4146 self._view.ui.btn_delete_delete_project.setEnabled(True) 4147 4148 def validate_delete_search(self) -> None: 4149 """Validates the input of the project name in real-time.""" 4150 if self._view.ui.list_delete_projects.currentItem() is not None: 4151 self._view.ui.list_delete_projects.currentItem().setSelected(False) 4152 # set color for lineEdit 4153 input_validator.InputValidator.validate_search_input( 4154 self._view.ui.list_delete_projects, 4155 self._view.ui.txt_delete_search, 4156 self._view.ui.lbl_delete_status_search, 4157 self._view.ui.txt_delete_selected_projects, 4158 ) 4159 4160 # </editor-fold> 4161 4162 # <editor-fold desc="View page"> 4163 def display_view_page(self) -> None: 4164 """Displays the edit project page.""" 4165 if self.is_distance_plot_open: 4166 self.distance_plot_dialog.close() 4167 self.is_distance_plot_open = False 4168 self._view.ui.list_view_project_proteins.clear() 4169 self._view.ui.txtedit_view_sequence.clear() 4170 # pre-process 4171 self._view.status_bar.showMessage(self._workspace_label.text()) 4172 # list all proteins from pdb directory 4173 gui_utils.fill_list_view_with_protein_names(self._current_project, self._view.ui.list_view_project_proteins) 4174 4175 tools.switch_page( 4176 self._view.ui.stackedWidget, 4177 self._view.ui.lbl_page_title, 4178 11, 4179 "View proteins of current project", 4180 ) 4181 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_view_page) 4182 gui_elements_to_hide = [ 4183 self._view.ui.btn_view_project_show, 4184 self._view.ui.btn_view_project_show_structure, 4185 self._view.ui.txtedit_view_sequence, 4186 self._view.ui.label_9, 4187 self._view.ui.label_11, 4188 ] 4189 gui_utils.hide_gui_elements(gui_elements_to_hide) 4190 4191 def view_show_options(self) -> None: 4192 """Controls which gui elements get shown.""" 4193 gui_elements_to_show = [ 4194 # self._view.ui.btn_view_project_show, 4195 self._view.ui.btn_view_project_show_structure, 4196 self._view.ui.txtedit_view_sequence, 4197 # self._view.ui.label_9, 4198 self._view.ui.label_11, 4199 ] 4200 gui_utils.show_gui_elements(gui_elements_to_show) 4201 self.view_sequence() 4202 4203 def view_sequence(self) -> None: 4204 """Displays the sequence of the selected protein in a text box.""" 4205 tmp_protein_basename = self._view.ui.list_view_project_proteins.currentItem().text() 4206 tmp_protein_sequences = self._current_project.search_protein(tmp_protein_basename).get_protein_sequences() 4207 self._view.ui.txtedit_view_sequence.clear() 4208 for tmp_sequence in tmp_protein_sequences: 4209 self._view.ui.txtedit_view_sequence.append("".join(tmp_sequence.sequence)) 4210 # fixme: experimental sequence viewer gui 4211 # dialog = dialog_sequence_viewer.SequenceViewer(tmp_protein_sequences, tmp_protein_filename) 4212 # dialog.exec_() 4213 4214 # </editor-fold> 4215 4216 # <editor-fold desc="Use page"> 4217 def validate_use_project_name(self) -> None: 4218 """Validates the input of the project name in real-time.""" 4219 input_validator.InputValidator.validate_project_name( 4220 self._view.ui.list_use_existing_projects, 4221 self._view.ui.txt_use_project_name, 4222 self._view.ui.lbl_use_status_project_name, 4223 self._view.ui.btn_use_next, 4224 ) 4225 4226 def validate_use_search(self) -> None: 4227 """Validates the input of the protein name in real-time.""" 4228 message = "Protein structure does not exists." 4229 input_validator.InputValidator.validate_search_input( 4230 self._view.ui.list_use_available_protein_structures, 4231 self._view.ui.txt_use_search, 4232 self._view.ui.lbl_use_status_search, 4233 status_message=message, 4234 ) 4235 4236 def add_protein_structure_to_new_project(self) -> None: 4237 """Adds the selected protein to the list which is used to create the new project.""" 4238 prot_to_add = self._view.ui.list_use_available_protein_structures.currentItem().text() 4239 self._view.ui.list_use_selected_protein_structures.addItem(prot_to_add) 4240 self._view.ui.list_use_available_protein_structures.takeItem( 4241 self._view.ui.list_use_available_protein_structures.currentRow(), 4242 ) 4243 self._view.ui.btn_use_add_available_protein_structures.setEnabled(False) 4244 if self._view.ui.list_use_available_protein_structures.count() > 0: 4245 try: 4246 self._view.ui.list_use_available_protein_structures.currentItem().setSelected(False) 4247 except AttributeError: 4248 constants.PYSSA_LOGGER.debug("No selection in use available proteins list on Use page.") 4249 4250 def remove_protein_structure_to_new_project(self) -> None: 4251 """Removes the selected protein from the list which is used to create the new project.""" 4252 prot_to_remove = self._view.ui.list_use_selected_protein_structures.currentItem() 4253 self._view.ui.list_use_selected_protein_structures.takeItem( 4254 self._view.ui.list_use_selected_protein_structures.currentRow(), 4255 ) 4256 self._view.ui.list_use_available_protein_structures.addItem(prot_to_remove) 4257 self._view.ui.btn_use_remove_selected_protein_structures.setEnabled(False) 4258 if self._view.ui.list_use_selected_protein_structures.count() > 0: 4259 try: 4260 self._view.ui.list_use_selected_protein_structures.currentItem().setSelected(False) 4261 except AttributeError: 4262 constants.PYSSA_LOGGER.debug("No selection in use selected proteins list on Use page.") 4263 4264 def show_protein_selection_for_use(self) -> None: 4265 """Shows the two lists for the protein selection.""" 4266 gui_elements_to_show = [ 4267 self._view.ui.lbl_use_search, 4268 self._view.ui.lbl_use_status_search, 4269 self._view.ui.txt_use_search, 4270 self._view.ui.btn_use_add_available_protein_structures, 4271 self._view.ui.lbl_use_available_protein_structures, 4272 self._view.ui.list_use_available_protein_structures, 4273 self._view.ui.btn_use_remove_selected_protein_structures, 4274 self._view.ui.lbl_use_selected_protein_structures, 4275 self._view.ui.list_use_selected_protein_structures, 4276 self._view.ui.btn_use_back, 4277 self._view.ui.btn_use_create_new_project, 4278 self._view.ui.lbl_use_new_project, 4279 ] 4280 gui_utils.show_gui_elements(gui_elements_to_show) 4281 self._view.ui.txt_use_project_name.setEnabled(False) 4282 gui_elements_to_hide = [ 4283 self._view.ui.btn_use_next, 4284 self._view.ui.list_use_existing_projects, 4285 ] 4286 gui_utils.hide_gui_elements(gui_elements_to_hide) 4287 gui_utils.disable_text_box(self._view.ui.txt_use_project_name, self._view.ui.lbl_use_project_name) 4288 self._view.ui.btn_use_add_available_protein_structures.setEnabled(False) 4289 self._view.ui.btn_use_remove_selected_protein_structures.setEnabled(False) 4290 4291 def hide_protein_selection_for_use(self) -> None: 4292 """Hides the two lists for the protein selection.""" 4293 gui_elements_to_show = [ 4294 self._view.ui.btn_use_next, 4295 self._view.ui.list_use_existing_projects, 4296 ] 4297 gui_utils.show_gui_elements(gui_elements_to_show) 4298 self._view.ui.txt_use_project_name.setEnabled(True) 4299 4300 gui_elements_to_hide = [ 4301 self._view.ui.lbl_use_search, 4302 self._view.ui.lbl_use_status_search, 4303 self._view.ui.txt_use_search, 4304 self._view.ui.btn_use_add_available_protein_structures, 4305 self._view.ui.lbl_use_available_protein_structures, 4306 self._view.ui.list_use_available_protein_structures, 4307 self._view.ui.btn_use_remove_selected_protein_structures, 4308 self._view.ui.lbl_use_selected_protein_structures, 4309 self._view.ui.list_use_selected_protein_structures, 4310 self._view.ui.btn_use_back, 4311 self._view.ui.btn_use_create_new_project, 4312 self._view.ui.lbl_use_new_project, 4313 ] 4314 gui_utils.hide_gui_elements(gui_elements_to_hide) 4315 gui_utils.enable_text_box(self._view.ui.txt_use_project_name, self._view.ui.lbl_use_project_name) 4316 4317 def use_enable_add(self) -> None: 4318 """Enables the add button.""" 4319 self._view.ui.btn_use_add_available_protein_structures.setEnabled(True) 4320 4321 def use_enable_remove(self) -> None: 4322 """Enables the remove button.""" 4323 self._view.ui.btn_use_remove_selected_protein_structures.setEnabled(True) 4324 4325 # </editor-fold> 4326 4327 # <editor-fold desc="ESM fold"> 4328 def _init_esm_pred_mono_page(self) -> None: 4329 """Clears all text boxes and sets up the default values for the page.""" 4330 # clears everything 4331 self._view.ui.txt_esm_prot_name.clear() 4332 self._view.ui.txt_esm_prot_seq.clear() 4333 for i in range(self._view.ui.table_esm_prot_to_predict.rowCount()): 4334 self._view.ui.table_esm_prot_to_predict.removeRow(i) 4335 # sets up defaults: Prediction 4336 self._view.ui.btn_esm_next.setEnabled(False) 4337 self._view.ui.btn_esm_next_2.setEnabled(False) 4338 self._view.ui.lbl_esm_prot_name_status.setText("") 4339 self._view.ui.lbl_esm_prot_seq_status.setText("") 4340 4341 def display_esm_pred_mono(self) -> None: 4342 """Displays the esm_fold monomer page.""" 4343 self._init_esm_pred_mono_page() 4344 gui_elements_to_show = [ 4345 self._view.ui.lbl_esm_prot_to_predict, 4346 self._view.ui.table_esm_prot_to_predict, 4347 self._view.ui.btn_esm_seq_to_predict, 4348 ] 4349 gui_elements_to_hide = [ 4350 self._view.ui.btn_esm_seq_to_predict_remove, 4351 self._view.ui.lbl_esm_prot_name, 4352 self._view.ui.txt_esm_prot_name, 4353 self._view.ui.lbl_esm_prot_name_status, 4354 self._view.ui.btn_esm_back, 4355 self._view.ui.btn_esm_next, 4356 self._view.ui.lbl_esm_prot_seq, 4357 self._view.ui.txt_esm_prot_seq, 4358 self._view.ui.lbl_esm_prot_seq_status, 4359 self._view.ui.btn_esm_back_2, 4360 self._view.ui.btn_esm_next_2, 4361 self._view.ui.btn_esm_predict, 4362 ] 4363 gui_utils.show_gui_elements(gui_elements_to_show) 4364 gui_utils.hide_gui_elements(gui_elements_to_hide) 4365 styles.color_button_not_ready(self._view.ui.btn_esm_next) 4366 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 1, "ESMFold Monomer Prediction") 4367 self.last_sidebar_button = styles.color_sidebar_buttons( 4368 self.last_sidebar_button, 4369 self._view.ui.btn_pred_cloud_monomer_page, 4370 ) 4371 4372 def cloud_esm_validate_protein_name(self) -> None: 4373 """Validates the input of the protein name in real-time.""" 4374 if safeguard.Safeguard.check_if_value_is_in_table_v_header( 4375 self._view.ui.txt_esm_prot_name.text(), 4376 self._view.ui.table_esm_prot_to_predict, 4377 ): 4378 self._view.ui.lbl_esm_prot_name_status.setText("Protein name already used.") 4379 self._view.ui.btn_esm_next.setEnabled(False) 4380 styles.color_button_not_ready(self._view.ui.btn_esm_next) 4381 else: 4382 self._view.ui.btn_esm_next.setEnabled(True) 4383 tools.validate_protein_name( 4384 self._view.ui.txt_esm_prot_name, 4385 self._view.ui.lbl_esm_prot_name_status, 4386 self._view.ui.btn_esm_next, 4387 ) 4388 4389 def cloud_esm_validate_protein_sequence(self) -> None: 4390 """Validates the input of the protein sequence in real-time.""" 4391 tools.validate_protein_sequence( 4392 self._view.ui.txt_esm_prot_seq, 4393 self._view.ui.lbl_esm_prot_seq_status, 4394 self._view.ui.btn_esm_next_2, 4395 ) 4396 4397 def setup_defaults_esm_monomer_prediction(self) -> None: 4398 """Sets up the default values for the page.""" 4399 # clears everything 4400 self._view.ui.txt_esm_prot_name.clear() 4401 self._view.ui.txt_esm_prot_seq.clear() 4402 # sets up defaults: Prediction 4403 self._view.ui.btn_esm_next.setEnabled(False) 4404 self._view.ui.btn_esm_next_2.setEnabled(False) 4405 self._view.ui.lbl_esm_prot_name_status.setText("") 4406 self._view.ui.lbl_esm_prot_seq_status.setText("") 4407 4408 def cloud_esm_add_seq_to_predict(self) -> None: 4409 """Shows the gui elements to add a sequence to the protein to predict.""" 4410 gui_elements_to_show = [ 4411 self._view.ui.lbl_esm_prot_to_predict, 4412 self._view.ui.table_esm_prot_to_predict, 4413 self._view.ui.lbl_esm_prot_name, 4414 self._view.ui.txt_esm_prot_name, 4415 self._view.ui.lbl_esm_prot_name_status, 4416 self._view.ui.btn_esm_back, 4417 self._view.ui.btn_esm_next, 4418 ] 4419 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4420 gui_elements_to_hide = [ 4421 self._view.ui.btn_esm_seq_to_predict_remove, 4422 self._view.ui.btn_esm_seq_to_predict, 4423 self._view.ui.lbl_esm_prot_seq, 4424 self._view.ui.txt_esm_prot_seq, 4425 self._view.ui.lbl_esm_prot_seq_status, 4426 self._view.ui.btn_esm_back_2, 4427 self._view.ui.btn_esm_next_2, 4428 self._view.ui.btn_esm_predict, 4429 ] 4430 gui_utils.disable_text_box(self._view.ui.txt_esm_prot_seq, self._view.ui.lbl_esm_prot_seq) 4431 gui_utils.show_gui_elements(gui_elements_to_show) 4432 gui_utils.hide_gui_elements(gui_elements_to_hide) 4433 self._view.ui.btn_esm_next.setEnabled(False) 4434 self._view.ui.txt_esm_prot_name.clear() 4435 styles.color_button_not_ready(self._view.ui.btn_esm_next) 4436 if self._view.ui.table_esm_prot_to_predict.rowCount() > 0: 4437 try: 4438 self._view.ui.table_esm_prot_to_predict.currentItem().setSelected(False) 4439 except AttributeError: 4440 constants.PYSSA_LOGGER.debug("No selection on Local Monomer Prediction in overview table.") 4441 4442 def cloud_esm_back(self) -> None: 4443 """Hides the gui elements for the protein name.""" 4444 gui_elements_to_show = [ 4445 self._view.ui.lbl_esm_prot_to_predict, 4446 self._view.ui.table_esm_prot_to_predict, 4447 self._view.ui.btn_esm_seq_to_predict_remove, 4448 self._view.ui.btn_esm_seq_to_predict, 4449 ] 4450 gui_elements_to_hide = [ 4451 self._view.ui.lbl_esm_prot_name, 4452 self._view.ui.txt_esm_prot_name, 4453 self._view.ui.lbl_esm_prot_name_status, 4454 self._view.ui.btn_esm_back, 4455 self._view.ui.btn_esm_next, 4456 self._view.ui.lbl_esm_prot_seq, 4457 self._view.ui.txt_esm_prot_seq, 4458 self._view.ui.lbl_esm_prot_seq_status, 4459 self._view.ui.btn_esm_back_2, 4460 self._view.ui.btn_esm_next_2, 4461 self._view.ui.btn_esm_predict, 4462 ] 4463 gui_utils.show_gui_elements(gui_elements_to_show) 4464 gui_utils.hide_gui_elements(gui_elements_to_hide) 4465 self.cloud_esm_check_if_table_is_empty() 4466 self._view.ui.btn_esm_seq_to_predict_remove.setEnabled(False) 4467 4468 def cloud_esm_next(self) -> None: 4469 """Shows the gui elements for the protein name.""" 4470 gui_elements_to_show = [ 4471 self._view.ui.lbl_esm_prot_to_predict, 4472 self._view.ui.table_esm_prot_to_predict, 4473 self._view.ui.lbl_esm_prot_name, 4474 self._view.ui.txt_esm_prot_name, 4475 self._view.ui.lbl_esm_prot_seq, 4476 self._view.ui.txt_esm_prot_seq, 4477 self._view.ui.lbl_esm_prot_seq_status, 4478 self._view.ui.btn_esm_back_2, 4479 self._view.ui.btn_esm_next_2, 4480 ] 4481 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_seq, self._view.ui.lbl_esm_prot_seq) 4482 gui_elements_to_hide = [ 4483 self._view.ui.btn_esm_seq_to_predict_remove, 4484 self._view.ui.btn_esm_seq_to_predict, 4485 self._view.ui.lbl_esm_prot_name_status, 4486 self._view.ui.btn_esm_back, 4487 self._view.ui.btn_esm_next, 4488 self._view.ui.btn_esm_predict, 4489 ] 4490 gui_utils.disable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4491 gui_utils.show_gui_elements(gui_elements_to_show) 4492 gui_utils.hide_gui_elements(gui_elements_to_hide) 4493 self._view.ui.txt_esm_prot_seq.clear() 4494 4495 def cloud_esm_back_2(self) -> None: 4496 """Hides the gui elements for the protein sequence.""" 4497 gui_elements_to_show = [ 4498 self._view.ui.lbl_esm_prot_to_predict, 4499 self._view.ui.table_esm_prot_to_predict, 4500 self._view.ui.lbl_esm_prot_name, 4501 self._view.ui.txt_esm_prot_name, 4502 self._view.ui.lbl_esm_prot_name_status, 4503 self._view.ui.btn_esm_back, 4504 self._view.ui.btn_esm_next, 4505 ] 4506 gui_elements_to_hide = [ 4507 self._view.ui.btn_esm_seq_to_predict_remove, 4508 self._view.ui.btn_esm_seq_to_predict, 4509 self._view.ui.lbl_esm_prot_seq, 4510 self._view.ui.txt_esm_prot_seq, 4511 self._view.ui.lbl_esm_prot_seq_status, 4512 self._view.ui.btn_esm_back_2, 4513 self._view.ui.btn_esm_next_2, 4514 self._view.ui.btn_esm_predict, 4515 ] 4516 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4517 gui_utils.disable_text_box(self._view.ui.txt_esm_prot_seq, self._view.ui.lbl_esm_prot_seq) 4518 gui_utils.show_gui_elements(gui_elements_to_show) 4519 gui_utils.hide_gui_elements(gui_elements_to_hide) 4520 4521 def cloud_esm_add_protein(self) -> None: 4522 """Adds protein to the list of proteins to predict.""" 4523 self._view.ui.table_esm_prot_to_predict.setRowCount(self._view.ui.table_esm_prot_to_predict.rowCount() + 1) 4524 self._view.ui.table_esm_prot_to_predict.insertRow(self._view.ui.table_esm_prot_to_predict.rowCount() + 1) 4525 self._view.ui.table_esm_prot_to_predict.setItem( 4526 self._view.ui.table_esm_prot_to_predict.rowCount() - 1, 4527 0, 4528 QtWidgets.QTableWidgetItem("A"), 4529 ) 4530 self._view.ui.table_esm_prot_to_predict.setItem( 4531 self._view.ui.table_esm_prot_to_predict.rowCount() - 1, 4532 1, 4533 QtWidgets.QTableWidgetItem(self._view.ui.txt_esm_prot_seq.toPlainText()), 4534 ) 4535 self._view.ui.table_esm_prot_to_predict.setVerticalHeaderItem( 4536 self._view.ui.table_esm_prot_to_predict.rowCount() - 1, 4537 QtWidgets.QTableWidgetItem(self._view.ui.txt_esm_prot_name.text()), 4538 ) 4539 self._view.ui.table_esm_prot_to_predict.resizeColumnsToContents() 4540 self.cloud_esm_check_if_table_is_empty() 4541 gui_elements_to_show = [ 4542 self._view.ui.lbl_esm_prot_to_predict, 4543 self._view.ui.table_esm_prot_to_predict, 4544 self._view.ui.btn_esm_seq_to_predict_remove, 4545 self._view.ui.btn_esm_seq_to_predict, 4546 self._view.ui.btn_esm_predict, 4547 ] 4548 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4549 gui_elements_to_hide = [ 4550 self._view.ui.lbl_esm_prot_name, 4551 self._view.ui.txt_esm_prot_name, 4552 self._view.ui.lbl_esm_prot_name_status, 4553 self._view.ui.btn_esm_back, 4554 self._view.ui.btn_esm_next, 4555 self._view.ui.lbl_esm_prot_seq, 4556 self._view.ui.txt_esm_prot_seq, 4557 self._view.ui.lbl_esm_prot_seq_status, 4558 self._view.ui.btn_esm_back_2, 4559 self._view.ui.btn_esm_next_2, 4560 ] 4561 gui_utils.show_gui_elements(gui_elements_to_show) 4562 gui_utils.hide_gui_elements(gui_elements_to_hide) 4563 self._view.ui.btn_esm_predict.setEnabled(True) 4564 self._view.ui.btn_esm_seq_to_predict_remove.setEnabled(False) 4565 self.setup_defaults_esm_monomer_prediction() 4566 4567 def cloud_esm_remove(self) -> None: 4568 """Removes a protein from the list of proteins to predict.""" 4569 self._view.ui.table_esm_prot_to_predict.removeRow(self._view.ui.table_esm_prot_to_predict.currentRow()) 4570 gui_elements_to_show = [ 4571 self._view.ui.lbl_esm_prot_to_predict, 4572 self._view.ui.table_esm_prot_to_predict, 4573 self._view.ui.btn_esm_seq_to_predict_remove, 4574 self._view.ui.btn_esm_seq_to_predict, 4575 self._view.ui.btn_esm_predict, 4576 ] 4577 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4578 gui_elements_to_hide = [ 4579 self._view.ui.lbl_esm_prot_name, 4580 self._view.ui.txt_esm_prot_name, 4581 self._view.ui.lbl_esm_prot_name_status, 4582 self._view.ui.btn_esm_back, 4583 self._view.ui.btn_esm_next, 4584 self._view.ui.lbl_esm_prot_seq, 4585 self._view.ui.txt_esm_prot_seq, 4586 self._view.ui.lbl_esm_prot_seq_status, 4587 self._view.ui.btn_esm_back_2, 4588 self._view.ui.btn_esm_next_2, 4589 ] 4590 gui_utils.show_gui_elements(gui_elements_to_show) 4591 gui_utils.hide_gui_elements(gui_elements_to_hide) 4592 self._view.ui.btn_esm_seq_to_predict_remove.setEnabled(False) 4593 self.cloud_esm_check_if_table_is_empty() 4594 4595 def cloud_esm_item_changed(self) -> None: 4596 """Enables the remove button.""" 4597 self._view.ui.btn_esm_seq_to_predict_remove.setEnabled(True) 4598 4599 def cloud_esm_check_if_table_is_empty(self) -> None: 4600 """Checks if the table proteins to predict is empty.""" 4601 if self._view.ui.table_esm_prot_to_predict.rowCount() == 0: 4602 styles.color_button_not_ready(self._view.ui.btn_esm_predict) 4603 self._view.ui.btn_esm_predict.setEnabled(False) 4604 gui_elements_to_show = [ 4605 self._view.ui.lbl_esm_prot_to_predict, 4606 self._view.ui.table_esm_prot_to_predict, 4607 self._view.ui.btn_esm_seq_to_predict, 4608 ] 4609 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4610 gui_elements_to_hide = [ 4611 self._view.ui.btn_esm_seq_to_predict_remove, 4612 self._view.ui.lbl_esm_prot_name, 4613 self._view.ui.txt_esm_prot_name, 4614 self._view.ui.lbl_esm_prot_name_status, 4615 self._view.ui.btn_esm_back, 4616 self._view.ui.btn_esm_next, 4617 self._view.ui.lbl_esm_prot_seq, 4618 self._view.ui.txt_esm_prot_seq, 4619 self._view.ui.lbl_esm_prot_seq_status, 4620 self._view.ui.btn_esm_back_2, 4621 self._view.ui.btn_esm_next_2, 4622 self._view.ui.btn_esm_predict, 4623 ] 4624 gui_utils.show_gui_elements(gui_elements_to_show) 4625 gui_utils.hide_gui_elements(gui_elements_to_hide) 4626 else: 4627 self._view.ui.btn_esm_predict.setEnabled(True) 4628 4629 # </editor-fold> 4630 4631 # <editor-fold desc="Monomer local prediction"> 4632 def _init_local_pred_mono_page(self) -> None: 4633 """Clears all text boxes and sets default values for the gui elements.""" 4634 # clears everything 4635 self._view.ui.txt_pred_mono_prot_name.clear() 4636 self._view.ui.txt_pred_mono_seq_name.clear() 4637 for i in range(self._view.ui.table_pred_mono_prot_to_predict.rowCount()): 4638 self._view.ui.table_pred_mono_prot_to_predict.removeRow(i) 4639 # sets up defaults: Prediction 4640 self._view.ui.btn_pred_mono_next.setEnabled(False) 4641 self._view.ui.btn_pred_mono_add_protein.setEnabled(False) 4642 self._view.ui.lbl_pred_mono_prot_name_status.setText("") 4643 self._view.ui.lbl_pred_mono_seq_name_status.setText("") 4644 4645 def display_local_pred_mono(self) -> None: 4646 """Displays the local prediction monomer page.""" 4647 # checks internet connection 4648 if not tools.check_internet_connectivity(): 4649 gui_utils.no_internet_dialog() 4650 return 4651 self._init_local_pred_mono_page() 4652 gui_elements_to_show = [ 4653 self._view.ui.lbl_pred_mono_prot_to_predict, 4654 self._view.ui.table_pred_mono_prot_to_predict, 4655 self._view.ui.btn_pred_mono_seq_to_predict, 4656 ] 4657 gui_elements_to_hide = [ 4658 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4659 self._view.ui.lbl_pred_mono_prot_name, 4660 self._view.ui.txt_pred_mono_prot_name, 4661 self._view.ui.lbl_pred_mono_prot_name_status, 4662 self._view.ui.btn_pred_mono_back, 4663 self._view.ui.btn_pred_mono_next, 4664 self._view.ui.lbl_pred_mono_seq_name, 4665 self._view.ui.txt_pred_mono_seq_name, 4666 self._view.ui.lbl_pred_mono_seq_name_status, 4667 self._view.ui.btn_pred_mono_back_2, 4668 self._view.ui.btn_pred_mono_add_protein, 4669 self._view.ui.lbl_pred_mono_advanced_config, 4670 self._view.ui.btn_pred_mono_advanced_config, 4671 self._view.ui.btn_pred_mono_predict, 4672 ] 4673 gui_utils.show_gui_elements(gui_elements_to_show) 4674 gui_utils.hide_gui_elements(gui_elements_to_hide) 4675 styles.color_button_not_ready(self._view.ui.btn_pred_mono_next) 4676 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 19, "Local Monomer Prediction") 4677 self.last_sidebar_button = styles.color_sidebar_buttons( 4678 self.last_sidebar_button, 4679 self._view.ui.btn_pred_local_monomer_page, 4680 ) 4681 4682 def local_pred_mono_validate_protein_name(self) -> None: 4683 """Validates the input of the protein name in real-time.""" 4684 if safeguard.Safeguard.check_if_value_is_in_table_v_header( 4685 self._view.ui.txt_pred_mono_prot_name.text(), 4686 self._view.ui.table_pred_mono_prot_to_predict, 4687 ): 4688 self._view.ui.lbl_pred_mono_prot_name_status.setText("Protein name already used.") 4689 self._view.ui.btn_pred_mono_next.setEnabled(False) 4690 styles.color_button_not_ready(self._view.ui.btn_pred_mono_next) 4691 else: 4692 self._view.ui.btn_pred_mono_next.setEnabled(True) 4693 tools.validate_protein_name( 4694 self._view.ui.txt_pred_mono_prot_name, 4695 self._view.ui.lbl_pred_mono_prot_name_status, 4696 self._view.ui.btn_pred_mono_next, 4697 ) 4698 4699 def local_pred_mono_validate_protein_sequence(self) -> None: 4700 """Validates the input of the protein sequence in real-time.""" 4701 tools.validate_protein_sequence( 4702 self._view.ui.txt_pred_mono_seq_name, 4703 self._view.ui.lbl_pred_mono_seq_name_status, 4704 self._view.ui.btn_pred_mono_add_protein, 4705 ) 4706 4707 def show_prediction_configuration(self) -> None: 4708 """Opens the prediction configuration dialog window.""" 4709 config = dialog_advanced_prediction_configurations.DialogAdvancedPredictionConfigurations( 4710 self.prediction_configuration, 4711 ) 4712 config.exec_() 4713 self.prediction_configuration.amber_force_field = config.prediction_config.amber_force_field 4714 self.prediction_configuration.templates = config.prediction_config.templates 4715 4716 def setup_defaults_monomer_prediction(self) -> None: 4717 """Sets up the defaults for the page.""" 4718 # clears everything 4719 self._view.ui.txt_pred_mono_prot_name.clear() 4720 self._view.ui.txt_pred_mono_seq_name.clear() 4721 # sets up defaults: Prediction 4722 self._view.ui.btn_pred_mono_next.setEnabled(False) 4723 self._view.ui.btn_pred_mono_add_protein.setEnabled(False) 4724 self._view.ui.lbl_pred_mono_prot_name_status.setText("") 4725 self._view.ui.lbl_pred_mono_seq_name_status.setText("") 4726 4727 def local_pred_mono_add_seq_to_predict(self) -> None: 4728 """Shows the gui elements for the protein name.""" 4729 gui_elements_to_show = [ 4730 self._view.ui.lbl_pred_mono_prot_to_predict, 4731 self._view.ui.table_pred_mono_prot_to_predict, 4732 self._view.ui.lbl_pred_mono_prot_name, 4733 self._view.ui.txt_pred_mono_prot_name, 4734 self._view.ui.lbl_pred_mono_prot_name_status, 4735 self._view.ui.btn_pred_mono_back, 4736 self._view.ui.btn_pred_mono_next, 4737 ] 4738 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4739 gui_elements_to_hide = [ 4740 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4741 self._view.ui.btn_pred_mono_seq_to_predict, 4742 self._view.ui.lbl_pred_mono_seq_name, 4743 self._view.ui.txt_pred_mono_seq_name, 4744 self._view.ui.lbl_pred_mono_seq_name_status, 4745 self._view.ui.btn_pred_mono_back_2, 4746 self._view.ui.btn_pred_mono_add_protein, 4747 self._view.ui.lbl_pred_mono_advanced_config, 4748 self._view.ui.btn_pred_mono_advanced_config, 4749 self._view.ui.btn_pred_mono_predict, 4750 ] 4751 gui_utils.disable_text_box(self._view.ui.txt_pred_mono_seq_name, self._view.ui.lbl_pred_mono_seq_name) 4752 gui_utils.show_gui_elements(gui_elements_to_show) 4753 gui_utils.hide_gui_elements(gui_elements_to_hide) 4754 self._view.ui.btn_pred_mono_next.setEnabled(False) 4755 self._view.ui.txt_pred_mono_prot_name.clear() 4756 styles.color_button_not_ready(self._view.ui.btn_pred_mono_next) 4757 if self._view.ui.table_pred_mono_prot_to_predict.rowCount() > 0: 4758 try: 4759 self._view.ui.table_pred_mono_prot_to_predict.currentItem().setSelected(False) 4760 except AttributeError: 4761 constants.PYSSA_LOGGER.debug("No selection on Local Monomer Prediction in overview table.") 4762 4763 def local_pred_mono_back(self) -> None: 4764 """Hides the gui elements for the protein name.""" 4765 gui_elements_to_show = [ 4766 self._view.ui.lbl_pred_mono_prot_to_predict, 4767 self._view.ui.table_pred_mono_prot_to_predict, 4768 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4769 self._view.ui.btn_pred_mono_seq_to_predict, 4770 ] 4771 gui_elements_to_hide = [ 4772 self._view.ui.lbl_pred_mono_prot_name, 4773 self._view.ui.txt_pred_mono_prot_name, 4774 self._view.ui.lbl_pred_mono_prot_name_status, 4775 self._view.ui.btn_pred_mono_back, 4776 self._view.ui.btn_pred_mono_next, 4777 self._view.ui.lbl_pred_mono_seq_name, 4778 self._view.ui.txt_pred_mono_seq_name, 4779 self._view.ui.lbl_pred_mono_seq_name_status, 4780 self._view.ui.btn_pred_mono_back_2, 4781 self._view.ui.btn_pred_mono_add_protein, 4782 self._view.ui.lbl_pred_mono_advanced_config, 4783 self._view.ui.btn_pred_mono_advanced_config, 4784 self._view.ui.btn_pred_mono_predict, 4785 ] 4786 gui_utils.show_gui_elements(gui_elements_to_show) 4787 gui_utils.hide_gui_elements(gui_elements_to_hide) 4788 self.local_pred_mono_check_if_table_is_empty() 4789 self._view.ui.btn_pred_mono_seq_to_predict_remove.setEnabled(False) 4790 4791 def local_pred_mono_next(self) -> None: 4792 """Shows the gui elements for the protein sequence.""" 4793 gui_elements_to_show = [ 4794 self._view.ui.lbl_pred_mono_prot_to_predict, 4795 self._view.ui.table_pred_mono_prot_to_predict, 4796 self._view.ui.lbl_pred_mono_prot_name, 4797 self._view.ui.txt_pred_mono_prot_name, 4798 self._view.ui.lbl_pred_mono_seq_name, 4799 self._view.ui.txt_pred_mono_seq_name, 4800 self._view.ui.lbl_pred_mono_seq_name_status, 4801 self._view.ui.btn_pred_mono_back_2, 4802 self._view.ui.btn_pred_mono_add_protein, 4803 ] 4804 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_seq_name, self._view.ui.lbl_pred_mono_seq_name) 4805 gui_elements_to_hide = [ 4806 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4807 self._view.ui.btn_pred_mono_seq_to_predict, 4808 self._view.ui.lbl_pred_mono_prot_name_status, 4809 self._view.ui.btn_pred_mono_back, 4810 self._view.ui.btn_pred_mono_next, 4811 self._view.ui.lbl_pred_mono_advanced_config, 4812 self._view.ui.btn_pred_mono_advanced_config, 4813 self._view.ui.btn_pred_mono_predict, 4814 ] 4815 gui_utils.disable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4816 gui_utils.show_gui_elements(gui_elements_to_show) 4817 gui_utils.hide_gui_elements(gui_elements_to_hide) 4818 self._view.ui.txt_pred_mono_seq_name.clear() 4819 4820 def local_pred_mono_back_2(self) -> None: 4821 """Hides the gui elements for the protein sequence.""" 4822 gui_elements_to_show = [ 4823 self._view.ui.lbl_pred_mono_prot_to_predict, 4824 self._view.ui.table_pred_mono_prot_to_predict, 4825 self._view.ui.lbl_pred_mono_prot_name, 4826 self._view.ui.txt_pred_mono_prot_name, 4827 self._view.ui.lbl_pred_mono_prot_name_status, 4828 self._view.ui.btn_pred_mono_back, 4829 self._view.ui.btn_pred_mono_next, 4830 ] 4831 gui_elements_to_hide = [ 4832 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4833 self._view.ui.btn_pred_mono_seq_to_predict, 4834 self._view.ui.lbl_pred_mono_seq_name, 4835 self._view.ui.txt_pred_mono_seq_name, 4836 self._view.ui.lbl_pred_mono_seq_name_status, 4837 self._view.ui.btn_pred_mono_back_2, 4838 self._view.ui.btn_pred_mono_add_protein, 4839 self._view.ui.lbl_pred_mono_advanced_config, 4840 self._view.ui.btn_pred_mono_advanced_config, 4841 self._view.ui.btn_pred_mono_predict, 4842 ] 4843 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4844 gui_utils.disable_text_box(self._view.ui.txt_pred_mono_seq_name, self._view.ui.lbl_pred_mono_seq_name) 4845 gui_utils.show_gui_elements(gui_elements_to_show) 4846 gui_utils.hide_gui_elements(gui_elements_to_hide) 4847 4848 def local_pred_mono_add_protein(self) -> None: 4849 """Adds protein to the list of proteins to predict.""" 4850 self._view.ui.table_pred_mono_prot_to_predict.setRowCount( 4851 self._view.ui.table_pred_mono_prot_to_predict.rowCount() + 1, 4852 ) 4853 self._view.ui.table_pred_mono_prot_to_predict.insertRow( 4854 self._view.ui.table_pred_mono_prot_to_predict.rowCount() + 1, 4855 ) 4856 self._view.ui.table_pred_mono_prot_to_predict.setItem( 4857 self._view.ui.table_pred_mono_prot_to_predict.rowCount() - 1, 4858 0, 4859 QtWidgets.QTableWidgetItem("A"), 4860 ) 4861 self._view.ui.table_pred_mono_prot_to_predict.setItem( 4862 self._view.ui.table_pred_mono_prot_to_predict.rowCount() - 1, 4863 1, 4864 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_mono_seq_name.toPlainText()), 4865 ) 4866 self._view.ui.table_pred_mono_prot_to_predict.setVerticalHeaderItem( 4867 self._view.ui.table_pred_mono_prot_to_predict.rowCount() - 1, 4868 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_mono_prot_name.text()), 4869 ) 4870 self._view.ui.table_pred_mono_prot_to_predict.resizeColumnsToContents() 4871 self.local_pred_mono_check_if_table_is_empty() 4872 gui_elements_to_show = [ 4873 self._view.ui.lbl_pred_mono_prot_to_predict, 4874 self._view.ui.table_pred_mono_prot_to_predict, 4875 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4876 self._view.ui.btn_pred_mono_seq_to_predict, 4877 self._view.ui.lbl_pred_mono_advanced_config, 4878 self._view.ui.btn_pred_mono_advanced_config, 4879 self._view.ui.btn_pred_mono_predict, 4880 ] 4881 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4882 gui_elements_to_hide = [ 4883 self._view.ui.lbl_pred_mono_prot_name, 4884 self._view.ui.txt_pred_mono_prot_name, 4885 self._view.ui.lbl_pred_mono_prot_name_status, 4886 self._view.ui.btn_pred_mono_back, 4887 self._view.ui.btn_pred_mono_next, 4888 self._view.ui.lbl_pred_mono_seq_name, 4889 self._view.ui.txt_pred_mono_seq_name, 4890 self._view.ui.lbl_pred_mono_seq_name_status, 4891 self._view.ui.btn_pred_mono_back_2, 4892 self._view.ui.btn_pred_mono_add_protein, 4893 ] 4894 gui_utils.show_gui_elements(gui_elements_to_show) 4895 gui_utils.hide_gui_elements(gui_elements_to_hide) 4896 self._view.ui.btn_pred_mono_predict.setEnabled(True) 4897 self._view.ui.btn_pred_mono_seq_to_predict_remove.setEnabled(False) 4898 self.setup_defaults_monomer_prediction() 4899 4900 def local_pred_mono_remove(self) -> None: 4901 """Removes the selected protein from the list of proteins to predict.""" 4902 self._view.ui.table_pred_mono_prot_to_predict.removeRow( 4903 self._view.ui.table_pred_mono_prot_to_predict.currentRow(), 4904 ) 4905 gui_elements_to_show = [ 4906 self._view.ui.lbl_pred_mono_prot_to_predict, 4907 self._view.ui.table_pred_mono_prot_to_predict, 4908 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4909 self._view.ui.btn_pred_mono_seq_to_predict, 4910 self._view.ui.lbl_pred_mono_advanced_config, 4911 self._view.ui.btn_pred_mono_advanced_config, 4912 self._view.ui.btn_pred_mono_predict, 4913 ] 4914 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4915 gui_elements_to_hide = [ 4916 self._view.ui.lbl_pred_mono_prot_name, 4917 self._view.ui.txt_pred_mono_prot_name, 4918 self._view.ui.lbl_pred_mono_prot_name_status, 4919 self._view.ui.btn_pred_mono_back, 4920 self._view.ui.btn_pred_mono_next, 4921 self._view.ui.lbl_pred_mono_seq_name, 4922 self._view.ui.txt_pred_mono_seq_name, 4923 self._view.ui.lbl_pred_mono_seq_name_status, 4924 self._view.ui.btn_pred_mono_back_2, 4925 self._view.ui.btn_pred_mono_add_protein, 4926 ] 4927 gui_utils.show_gui_elements(gui_elements_to_show) 4928 gui_utils.hide_gui_elements(gui_elements_to_hide) 4929 self._view.ui.btn_pred_mono_seq_to_predict_remove.setEnabled(False) 4930 self.local_pred_mono_check_if_table_is_empty() 4931 4932 def local_pred_mono_item_changed(self) -> None: 4933 """Enables the remove button.""" 4934 self._view.ui.btn_pred_mono_seq_to_predict_remove.setEnabled(True) 4935 4936 def local_pred_mono_check_if_table_is_empty(self) -> None: 4937 """Checks if the table proteins to predict is empty.""" 4938 if self._view.ui.table_pred_mono_prot_to_predict.rowCount() == 0: 4939 styles.color_button_not_ready(self._view.ui.btn_pred_mono_predict) 4940 self._view.ui.btn_pred_mono_predict.setEnabled(False) 4941 gui_elements_to_show = [ 4942 self._view.ui.lbl_pred_mono_prot_to_predict, 4943 self._view.ui.table_pred_mono_prot_to_predict, 4944 self._view.ui.btn_pred_mono_seq_to_predict, 4945 ] 4946 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4947 gui_elements_to_hide = [ 4948 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4949 self._view.ui.lbl_pred_mono_prot_name, 4950 self._view.ui.txt_pred_mono_prot_name, 4951 self._view.ui.lbl_pred_mono_prot_name_status, 4952 self._view.ui.btn_pred_mono_back, 4953 self._view.ui.btn_pred_mono_next, 4954 self._view.ui.lbl_pred_mono_seq_name, 4955 self._view.ui.txt_pred_mono_seq_name, 4956 self._view.ui.lbl_pred_mono_seq_name_status, 4957 self._view.ui.btn_pred_mono_back_2, 4958 self._view.ui.btn_pred_mono_add_protein, 4959 self._view.ui.lbl_pred_mono_advanced_config, 4960 self._view.ui.btn_pred_mono_advanced_config, 4961 self._view.ui.btn_pred_mono_predict, 4962 ] 4963 gui_utils.show_gui_elements(gui_elements_to_show) 4964 gui_utils.hide_gui_elements(gui_elements_to_hide) 4965 else: 4966 self._view.ui.btn_pred_mono_predict.setEnabled(True) 4967 4968 # </editor-fold> 4969 4970 # <editor-fold desc="Multimer local prediction"> 4971 def _init_local_pred_multi_page(self) -> None: 4972 """Clears all text boxes and sets default values for the gui elements.""" 4973 # clears everything 4974 self._view.ui.txt_pred_multi_prot_name.clear() 4975 self._view.ui.txt_pred_multi_prot_seq.clear() 4976 self._view.ui.list_pred_multi_prot_seq_overview.clear() 4977 # sets up defaults: Prediction 4978 self._view.ui.btn_pred_multi_next.setEnabled(False) 4979 self._view.ui.btn_pred_multi_prot_to_predict_add_2.setEnabled(False) 4980 self._view.ui.lbl_pred_multi_prot_name_status.setText("") 4981 self._view.ui.lbl_pred_multi_prot_seq_status.setText("") 4982 4983 def display_local_pred_multi(self) -> None: 4984 """Displays the local prediction multimer page.""" 4985 # checks internet connection 4986 if not tools.check_internet_connectivity(): 4987 gui_utils.no_internet_dialog() 4988 return 4989 4990 gui_elements_to_show = [ 4991 self._view.ui.lbl_pred_multi_prot_to_predict, 4992 self._view.ui.table_pred_multi_prot_to_predict, 4993 self._view.ui.btn_pred_multi_prot_to_predict_add, 4994 ] 4995 gui_elements_to_hide = [ 4996 self._view.ui.btn_pred_multi_prot_to_predict_remove, 4997 self._view.ui.lbl_pred_multi_prot_name_status, 4998 self._view.ui.btn_pred_multi_back, 4999 self._view.ui.btn_pred_multi_next, 5000 self._view.ui.lbl_pred_multi_prot_name, 5001 self._view.ui.txt_pred_multi_prot_name, 5002 self._view.ui.lbl_pred_multi_prot_seq, 5003 self._view.ui.txt_pred_multi_prot_seq, 5004 self._view.ui.lbl_pred_multi_prot_seq_status, 5005 self._view.ui.lbl_pred_multi_prot_seq_add, 5006 self._view.ui.btn_pred_multi_prot_seq_add, 5007 self._view.ui.lbl_pred_multi_prot_seq_overview, 5008 self._view.ui.list_pred_multi_prot_seq_overview, 5009 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5010 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5011 self._view.ui.btn_pred_multi_back_2, 5012 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5013 self._view.ui.lbl_pred_multi_advanced_config, 5014 self._view.ui.btn_pred_multi_advanced_config, 5015 self._view.ui.btn_pred_multi_predict, 5016 ] 5017 for i in range(self._view.ui.table_pred_multi_prot_to_predict.rowCount() - 1, -1, -1): 5018 self._view.ui.table_pred_multi_prot_to_predict.removeRow(i) 5019 gui_utils.show_gui_elements(gui_elements_to_show) 5020 gui_utils.hide_gui_elements(gui_elements_to_hide) 5021 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 20, "Local Multimer Prediction") 5022 self.last_sidebar_button = styles.color_sidebar_buttons( 5023 self.last_sidebar_button, 5024 self._view.ui.btn_pred_local_multimer_page, 5025 ) 5026 5027 def local_pred_multi_validate_protein_name(self) -> None: 5028 """Validates the input of the protein name in real-time.""" 5029 if safeguard.Safeguard.check_if_value_is_in_table_v_header( 5030 self._view.ui.txt_pred_multi_prot_name.text(), 5031 self._view.ui.table_pred_multi_prot_to_predict, 5032 ): 5033 self._view.ui.lbl_pred_multi_prot_name_status.setText("Protein name already used.") 5034 self._view.ui.btn_pred_multi_next.setEnabled(False) 5035 styles.color_button_not_ready(self._view.ui.btn_pred_multi_next) 5036 else: 5037 self._view.ui.btn_pred_multi_next.setEnabled(True) 5038 tools.validate_protein_name( 5039 self._view.ui.txt_pred_multi_prot_name, 5040 self._view.ui.lbl_pred_multi_prot_name_status, 5041 self._view.ui.btn_pred_multi_next, 5042 ) 5043 5044 def local_pred_multi_validate_protein_sequence(self) -> None: 5045 """Validates the input of the protein sequence in real-time.""" 5046 tools.validate_protein_sequence( 5047 self._view.ui.txt_pred_multi_prot_seq, 5048 self._view.ui.lbl_pred_multi_prot_seq_status, 5049 self._view.ui.btn_pred_multi_prot_seq_add, 5050 ) 5051 5052 def local_pred_multi_check_if_table_is_empty(self) -> None: 5053 """Checks if the table proteins to predict is empty.""" 5054 if self._view.ui.table_pred_multi_prot_to_predict.rowCount() == 0: 5055 styles.color_button_not_ready(self._view.ui.btn_pred_multi_predict) 5056 self._view.ui.btn_pred_multi_predict.setEnabled(False) 5057 gui_elements_to_show = [ 5058 self._view.ui.lbl_pred_multi_prot_to_predict, 5059 self._view.ui.table_pred_multi_prot_to_predict, 5060 self._view.ui.btn_pred_multi_prot_to_predict_add, 5061 ] 5062 gui_elements_to_hide = [ 5063 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5064 self._view.ui.lbl_pred_multi_prot_name_status, 5065 self._view.ui.btn_pred_multi_back, 5066 self._view.ui.btn_pred_multi_next, 5067 self._view.ui.lbl_pred_multi_prot_name, 5068 self._view.ui.txt_pred_multi_prot_name, 5069 self._view.ui.lbl_pred_multi_prot_seq, 5070 self._view.ui.txt_pred_multi_prot_seq, 5071 self._view.ui.lbl_pred_multi_prot_seq_status, 5072 self._view.ui.lbl_pred_multi_prot_seq_add, 5073 self._view.ui.btn_pred_multi_prot_seq_add, 5074 self._view.ui.lbl_pred_multi_prot_seq_overview, 5075 self._view.ui.list_pred_multi_prot_seq_overview, 5076 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5077 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5078 self._view.ui.btn_pred_multi_back_2, 5079 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5080 self._view.ui.lbl_pred_multi_advanced_config, 5081 self._view.ui.btn_pred_multi_advanced_config, 5082 self._view.ui.btn_pred_multi_predict, 5083 ] 5084 gui_utils.show_gui_elements(gui_elements_to_show) 5085 gui_utils.hide_gui_elements(gui_elements_to_hide) 5086 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False) 5087 else: 5088 self._view.ui.btn_pred_multi_predict.setEnabled(True) 5089 gui_elements_to_show = [ 5090 self._view.ui.lbl_pred_multi_prot_to_predict, 5091 self._view.ui.table_pred_multi_prot_to_predict, 5092 self._view.ui.btn_pred_multi_prot_to_predict_add, 5093 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5094 self._view.ui.lbl_pred_multi_advanced_config, 5095 self._view.ui.btn_pred_multi_advanced_config, 5096 self._view.ui.btn_pred_multi_predict, 5097 ] 5098 gui_elements_to_hide = [ 5099 self._view.ui.lbl_pred_multi_prot_name_status, 5100 self._view.ui.btn_pred_multi_back, 5101 self._view.ui.btn_pred_multi_next, 5102 self._view.ui.lbl_pred_multi_prot_name, 5103 self._view.ui.txt_pred_multi_prot_name, 5104 self._view.ui.lbl_pred_multi_prot_seq, 5105 self._view.ui.txt_pred_multi_prot_seq, 5106 self._view.ui.lbl_pred_multi_prot_seq_status, 5107 self._view.ui.lbl_pred_multi_prot_seq_add, 5108 self._view.ui.btn_pred_multi_prot_seq_add, 5109 self._view.ui.lbl_pred_multi_prot_seq_overview, 5110 self._view.ui.list_pred_multi_prot_seq_overview, 5111 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5112 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5113 self._view.ui.btn_pred_multi_back_2, 5114 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5115 ] 5116 gui_utils.show_gui_elements(gui_elements_to_show) 5117 gui_utils.hide_gui_elements(gui_elements_to_hide) 5118 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False) 5119 5120 def local_pred_multi_add_sequence_to_list(self) -> None: 5121 """Adds the entered sequence to the list of sequences of the protein.""" 5122 self._view.ui.list_pred_multi_prot_seq_overview.addItem( 5123 QtWidgets.QListWidgetItem(self._view.ui.txt_pred_multi_prot_seq.toPlainText()), 5124 ) 5125 self.local_pred_multi_check_if_list_is_empty() 5126 5127 def local_pred_multi_remove_sequence_to_list(self) -> None: 5128 """Removes the entered sequence to the list of sequences of the protein.""" 5129 self._view.ui.list_pred_multi_prot_seq_overview.takeItem( 5130 self._view.ui.list_pred_multi_prot_seq_overview.currentRow(), 5131 ) 5132 self.local_pred_multi_check_if_list_is_empty() 5133 self._view.ui.btn_pred_multi_prot_seq_overview_remove.setEnabled(False) 5134 5135 def local_pred_multi_check_if_list_is_empty(self) -> None: 5136 """Checks if the list of sequences of the protein is empty.""" 5137 if self._view.ui.list_pred_multi_prot_seq_overview.count() == 0: 5138 self._view.ui.btn_pred_multi_prot_to_predict_add_2.setEnabled(False) 5139 else: 5140 self._view.ui.btn_pred_multi_prot_to_predict_add_2.setEnabled(True) 5141 5142 def local_pred_multi_add(self) -> None: 5143 """Shows the gui elements for the protein name.""" 5144 gui_elements_to_show = [ 5145 self._view.ui.lbl_pred_multi_prot_to_predict, 5146 self._view.ui.table_pred_multi_prot_to_predict, 5147 self._view.ui.lbl_pred_multi_prot_name, 5148 self._view.ui.txt_pred_multi_prot_name, 5149 self._view.ui.lbl_pred_multi_prot_name_status, 5150 self._view.ui.btn_pred_multi_back, 5151 self._view.ui.btn_pred_multi_next, 5152 ] 5153 gui_elements_to_hide = [ 5154 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5155 self._view.ui.btn_pred_multi_prot_to_predict_add, 5156 self._view.ui.lbl_pred_multi_prot_seq, 5157 self._view.ui.txt_pred_multi_prot_seq, 5158 self._view.ui.lbl_pred_multi_prot_seq_status, 5159 self._view.ui.lbl_pred_multi_prot_seq_add, 5160 self._view.ui.btn_pred_multi_prot_seq_add, 5161 self._view.ui.lbl_pred_multi_prot_seq_overview, 5162 self._view.ui.list_pred_multi_prot_seq_overview, 5163 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5164 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5165 self._view.ui.btn_pred_multi_back_2, 5166 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5167 self._view.ui.lbl_pred_multi_advanced_config, 5168 self._view.ui.btn_pred_multi_advanced_config, 5169 self._view.ui.btn_pred_multi_predict, 5170 ] 5171 gui_utils.show_gui_elements(gui_elements_to_show) 5172 gui_utils.hide_gui_elements(gui_elements_to_hide) 5173 gui_utils.enable_text_box(self._view.ui.txt_pred_multi_prot_name, self._view.ui.lbl_pred_multi_prot_name) 5174 gui_utils.disable_text_box(self._view.ui.txt_pred_multi_prot_seq, self._view.ui.lbl_pred_multi_prot_seq) 5175 self._view.ui.btn_pred_multi_next.setEnabled(False) 5176 self._view.ui.txt_pred_multi_prot_name.clear() 5177 styles.color_button_not_ready(self._view.ui.btn_pred_multi_next) 5178 if self._view.ui.table_pred_multi_prot_to_predict.rowCount() > 0: 5179 try: 5180 self._view.ui.table_pred_multi_prot_to_predict.currentItem().setSelected(False) 5181 except AttributeError: 5182 constants.PYSSA_LOGGER.debug("No selection on Local Multimer Prediction in overview table.") 5183 5184 def local_pred_multi_back(self) -> None: 5185 """Hides the gui elements for the protein name.""" 5186 gui_elements_to_show = [ 5187 self._view.ui.lbl_pred_multi_prot_to_predict, 5188 self._view.ui.table_pred_multi_prot_to_predict, 5189 self._view.ui.btn_pred_multi_prot_to_predict_add, 5190 ] 5191 gui_elements_to_hide = [ 5192 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5193 self._view.ui.lbl_pred_multi_prot_name, 5194 self._view.ui.txt_pred_multi_prot_name, 5195 self._view.ui.lbl_pred_multi_prot_name_status, 5196 self._view.ui.btn_pred_multi_back, 5197 self._view.ui.btn_pred_multi_next, 5198 self._view.ui.lbl_pred_multi_prot_seq, 5199 self._view.ui.txt_pred_multi_prot_seq, 5200 self._view.ui.lbl_pred_multi_prot_seq_status, 5201 self._view.ui.lbl_pred_multi_prot_seq_add, 5202 self._view.ui.btn_pred_multi_prot_seq_add, 5203 self._view.ui.lbl_pred_multi_prot_seq_overview, 5204 self._view.ui.list_pred_multi_prot_seq_overview, 5205 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5206 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5207 self._view.ui.btn_pred_multi_back_2, 5208 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5209 self._view.ui.lbl_pred_multi_advanced_config, 5210 self._view.ui.btn_pred_multi_advanced_config, 5211 self._view.ui.btn_pred_multi_predict, 5212 ] 5213 gui_utils.show_gui_elements(gui_elements_to_show) 5214 gui_utils.hide_gui_elements(gui_elements_to_hide) 5215 self.local_pred_multi_check_if_table_is_empty() 5216 5217 def local_pred_multi_next(self) -> None: 5218 """Shows the gui elements for the protein sequence.""" 5219 gui_elements_to_show = [ 5220 self._view.ui.lbl_pred_multi_prot_to_predict, 5221 self._view.ui.table_pred_multi_prot_to_predict, 5222 self._view.ui.lbl_pred_multi_prot_name, 5223 self._view.ui.txt_pred_multi_prot_name, 5224 self._view.ui.lbl_pred_multi_prot_seq, 5225 self._view.ui.txt_pred_multi_prot_seq, 5226 self._view.ui.lbl_pred_multi_prot_seq_status, 5227 self._view.ui.lbl_pred_multi_prot_seq_add, 5228 self._view.ui.btn_pred_multi_prot_seq_add, 5229 self._view.ui.lbl_pred_multi_prot_seq_overview, 5230 self._view.ui.list_pred_multi_prot_seq_overview, 5231 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5232 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5233 self._view.ui.btn_pred_multi_back_2, 5234 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5235 ] 5236 gui_elements_to_hide = [ 5237 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5238 self._view.ui.btn_pred_multi_prot_to_predict_add, 5239 self._view.ui.lbl_pred_multi_prot_name_status, 5240 self._view.ui.btn_pred_multi_back, 5241 self._view.ui.btn_pred_multi_next, 5242 self._view.ui.lbl_pred_multi_advanced_config, 5243 self._view.ui.btn_pred_multi_advanced_config, 5244 self._view.ui.btn_pred_multi_predict, 5245 ] 5246 gui_utils.show_gui_elements(gui_elements_to_show) 5247 gui_utils.hide_gui_elements(gui_elements_to_hide) 5248 gui_utils.enable_text_box(self._view.ui.txt_pred_multi_prot_seq, self._view.ui.lbl_pred_multi_prot_seq) 5249 gui_utils.disable_text_box(self._view.ui.txt_pred_multi_prot_name, self._view.ui.lbl_pred_multi_prot_name) 5250 self._view.ui.txt_pred_multi_prot_seq.clear() 5251 self._view.ui.list_pred_multi_prot_seq_overview.clear() 5252 self._view.ui.btn_pred_multi_prot_to_predict_add_2.setEnabled(False) 5253 self._view.ui.btn_pred_multi_prot_seq_overview_remove.setEnabled(False) 5254 styles.color_button_not_ready(self._view.ui.btn_pred_multi_prot_to_predict_add_2) 5255 5256 def local_pred_multi_back_2(self) -> None: 5257 """Hides the gui elements for the protein sequence.""" 5258 gui_elements_to_show = [ 5259 self._view.ui.lbl_pred_multi_prot_to_predict, 5260 self._view.ui.table_pred_multi_prot_to_predict, 5261 self._view.ui.lbl_pred_multi_prot_name_status, 5262 self._view.ui.btn_pred_multi_back, 5263 self._view.ui.btn_pred_multi_next, 5264 self._view.ui.lbl_pred_multi_prot_name, 5265 self._view.ui.txt_pred_multi_prot_name, 5266 ] 5267 gui_elements_to_hide = [ 5268 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5269 self._view.ui.btn_pred_multi_prot_to_predict_add, 5270 self._view.ui.lbl_pred_multi_prot_seq, 5271 self._view.ui.txt_pred_multi_prot_seq, 5272 self._view.ui.lbl_pred_multi_prot_seq_status, 5273 self._view.ui.lbl_pred_multi_prot_seq_add, 5274 self._view.ui.btn_pred_multi_prot_seq_add, 5275 self._view.ui.lbl_pred_multi_prot_seq_overview, 5276 self._view.ui.list_pred_multi_prot_seq_overview, 5277 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5278 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5279 self._view.ui.btn_pred_multi_back_2, 5280 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5281 self._view.ui.lbl_pred_multi_advanced_config, 5282 self._view.ui.btn_pred_multi_advanced_config, 5283 self._view.ui.btn_pred_multi_predict, 5284 ] 5285 gui_utils.show_gui_elements(gui_elements_to_show) 5286 gui_utils.hide_gui_elements(gui_elements_to_hide) 5287 gui_utils.enable_text_box(self._view.ui.txt_pred_multi_prot_name, self._view.ui.lbl_pred_multi_prot_name) 5288 gui_utils.disable_text_box(self._view.ui.txt_pred_multi_prot_seq, self._view.ui.lbl_pred_multi_prot_seq) 5289 5290 def local_pred_multi_prot_seq_overview_item_changed(self) -> None: 5291 """Enables the remove button of the list sequences of the protein.""" 5292 self._view.ui.btn_pred_multi_prot_seq_overview_remove.setEnabled(True) 5293 5294 def local_pred_multi_prot_to_predict_item_changed(self) -> None: 5295 """Enables the remove button of the table proteins to predict.""" 5296 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(True) 5297 5298 def local_pred_multi_prot_to_predict_add_2(self) -> None: 5299 """Adds the protein to the list of proteins to predict.""" 5300 for i in range(self._view.ui.list_pred_multi_prot_seq_overview.count()): 5301 self._view.ui.table_pred_multi_prot_to_predict.setRowCount( 5302 self._view.ui.table_pred_multi_prot_to_predict.rowCount() + 1, 5303 ) 5304 self._view.ui.table_pred_multi_prot_to_predict.insertRow( 5305 self._view.ui.table_pred_multi_prot_to_predict.rowCount() + 1, 5306 ) 5307 tmp_chain_seq = ( 5308 constants.chain_dict.get(i), 5309 self._view.ui.list_pred_multi_prot_seq_overview.item(i).text(), 5310 ) 5311 self._view.ui.table_pred_multi_prot_to_predict.setItem( 5312 self._view.ui.table_pred_multi_prot_to_predict.rowCount() - 1, 5313 0, 5314 QtWidgets.QTableWidgetItem(tmp_chain_seq[0]), 5315 ) 5316 self._view.ui.table_pred_multi_prot_to_predict.setItem( 5317 self._view.ui.table_pred_multi_prot_to_predict.rowCount() - 1, 5318 1, 5319 QtWidgets.QTableWidgetItem(tmp_chain_seq[1]), 5320 ) 5321 name_item = QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_multi_prot_name.text()) 5322 self._view.ui.table_pred_multi_prot_to_predict.setVerticalHeaderItem( 5323 self._view.ui.table_pred_multi_prot_to_predict.rowCount() - 1, 5324 name_item, 5325 ) 5326 self._view.ui.table_pred_multi_prot_to_predict.resizeColumnsToContents() 5327 self.local_pred_multi_check_if_table_is_empty() 5328 gui_elements_to_show = [ 5329 self._view.ui.lbl_pred_multi_prot_to_predict, 5330 self._view.ui.table_pred_multi_prot_to_predict, 5331 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5332 self._view.ui.btn_pred_multi_prot_to_predict_add, 5333 self._view.ui.lbl_pred_multi_advanced_config, 5334 self._view.ui.btn_pred_multi_advanced_config, 5335 self._view.ui.btn_pred_multi_predict, 5336 ] 5337 gui_elements_to_hide = [ 5338 self._view.ui.lbl_pred_multi_prot_name_status, 5339 self._view.ui.btn_pred_multi_back, 5340 self._view.ui.btn_pred_multi_next, 5341 self._view.ui.lbl_pred_multi_prot_name, 5342 self._view.ui.txt_pred_multi_prot_name, 5343 self._view.ui.lbl_pred_multi_prot_seq, 5344 self._view.ui.txt_pred_multi_prot_seq, 5345 self._view.ui.lbl_pred_multi_prot_seq_status, 5346 self._view.ui.lbl_pred_multi_prot_seq_add, 5347 self._view.ui.btn_pred_multi_prot_seq_add, 5348 self._view.ui.lbl_pred_multi_prot_seq_overview, 5349 self._view.ui.list_pred_multi_prot_seq_overview, 5350 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5351 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5352 self._view.ui.btn_pred_multi_back_2, 5353 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5354 ] 5355 gui_utils.show_gui_elements(gui_elements_to_show) 5356 gui_utils.hide_gui_elements(gui_elements_to_hide) 5357 self._init_local_pred_multi_page() 5358 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False) 5359 5360 def local_pred_multi_remove(self) -> None: 5361 """Removes the selected protein from the list of proteins to predict.""" 5362 self._view.ui.table_pred_multi_prot_to_predict.removeRow( 5363 self._view.ui.table_pred_multi_prot_to_predict.currentRow(), 5364 ) 5365 if self._view.ui.table_pred_multi_prot_to_predict.rowCount() > 0: 5366 prot_name = self._view.ui.table_pred_multi_prot_to_predict.verticalHeaderItem( 5367 self._view.ui.table_pred_multi_prot_to_predict.currentRow(), 5368 ).text() 5369 for i in range(self._view.ui.table_pred_multi_prot_to_predict.rowCount()): 5370 if self._view.ui.table_pred_multi_prot_to_predict.verticalHeaderItem(i).text() == prot_name: 5371 self._view.ui.table_pred_multi_prot_to_predict.setItem( 5372 i, 5373 0, 5374 QtWidgets.QTableWidgetItem(constants.chain_dict.get(i)), 5375 ) 5376 self.local_pred_multi_check_if_table_is_empty() 5377 gui_elements_to_show = [ 5378 self._view.ui.lbl_pred_multi_prot_to_predict, 5379 self._view.ui.table_pred_multi_prot_to_predict, 5380 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5381 self._view.ui.btn_pred_multi_prot_to_predict_add, 5382 self._view.ui.lbl_pred_multi_advanced_config, 5383 self._view.ui.btn_pred_multi_advanced_config, 5384 self._view.ui.btn_pred_multi_predict, 5385 ] 5386 gui_elements_to_hide = [ 5387 self._view.ui.lbl_pred_multi_prot_name_status, 5388 self._view.ui.btn_pred_multi_back, 5389 self._view.ui.btn_pred_multi_next, 5390 self._view.ui.lbl_pred_multi_prot_name, 5391 self._view.ui.txt_pred_multi_prot_name, 5392 self._view.ui.lbl_pred_multi_prot_seq, 5393 self._view.ui.txt_pred_multi_prot_seq, 5394 self._view.ui.lbl_pred_multi_prot_seq_status, 5395 self._view.ui.lbl_pred_multi_prot_seq_add, 5396 self._view.ui.btn_pred_multi_prot_seq_add, 5397 self._view.ui.lbl_pred_multi_prot_seq_overview, 5398 self._view.ui.list_pred_multi_prot_seq_overview, 5399 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5400 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5401 self._view.ui.btn_pred_multi_back_2, 5402 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5403 ] 5404 gui_utils.show_gui_elements(gui_elements_to_show) 5405 gui_utils.hide_gui_elements(gui_elements_to_hide) 5406 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False) 5407 self.local_pred_multi_check_if_table_is_empty() 5408 5409 # </editor-fold> 5410 5411 # <editor-fold desc="Monomer prediction + analysis"> 5412 def _init_mono_pred_analysis_page(self) -> None: 5413 """Clears all text boxes and sets default values for the gui elements.""" 5414 # <editor-fold desc="Prediction section"> 5415 self._view.ui.txt_pred_analysis_mono_prot_name.clear() 5416 self._view.ui.txt_pred_analysis_mono_seq_name.clear() 5417 for i in range(self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount()): 5418 self._view.ui.table_pred_analysis_mono_prot_to_predict.removeRow(i) 5419 # sets up defaults: Prediction 5420 self._view.ui.btn_pred_analysis_mono_next.setEnabled(False) 5421 self._view.ui.btn_pred_analysis_mono_add_protein.setEnabled(False) 5422 self._view.ui.lbl_pred_analysis_mono_prot_name_status.setText("") 5423 self._view.ui.lbl_pred_analysis_mono_seq_name_status.setText("") 5424 5425 # </editor-fold> 5426 5427 # <editor-fold desc="Analysis section"> 5428 self._view.ui.list_pred_analysis_mono_overview.clear() 5429 self._view.ui.btn_pred_analysis_mono_remove.hide() 5430 5431 # </editor-fold> 5432 5433 def display_monomer_pred_analysis(self) -> None: 5434 """Displays the monomer prediction + analysis page.""" 5435 # checks internet connection 5436 if not tools.check_internet_connectivity(): 5437 gui_utils.no_internet_dialog() 5438 return 5439 5440 self._init_mono_pred_analysis_page() 5441 self._view.ui.table_pred_analysis_mono_prot_to_predict.clear() 5442 self._view.ui.table_pred_analysis_mono_prot_to_predict.setHorizontalHeaderItem( 5443 0, 5444 QtWidgets.QTableWidgetItem("Chain"), 5445 ) 5446 self._view.ui.table_pred_analysis_mono_prot_to_predict.setHorizontalHeaderItem( 5447 1, 5448 QtWidgets.QTableWidgetItem("Sequence"), 5449 ) 5450 self._view.ui.table_pred_analysis_mono_prot_to_predict.resizeColumnsToContents() 5451 gui_elements_to_show = [ 5452 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5453 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5454 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5455 ] 5456 gui_elements_to_hide = [ 5457 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5458 self._view.ui.lbl_pred_analysis_mono_prot_name, 5459 self._view.ui.txt_pred_analysis_mono_prot_name, 5460 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5461 self._view.ui.btn_pred_analysis_mono_back, 5462 self._view.ui.btn_pred_analysis_mono_next, 5463 self._view.ui.lbl_pred_analysis_mono_seq_name, 5464 self._view.ui.txt_pred_analysis_mono_seq_name, 5465 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5466 self._view.ui.btn_pred_analysis_mono_back_2, 5467 self._view.ui.btn_pred_analysis_mono_add_protein, 5468 self._view.ui.lbl_pred_mono_advanced_config_2, 5469 self._view.ui.btn_pred_mono_advanced_config_2, 5470 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5471 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5472 ] 5473 gui_utils.show_gui_elements(gui_elements_to_show) 5474 gui_utils.hide_gui_elements(gui_elements_to_hide) 5475 if self._view.ui.tabWidget.currentIndex() == 1: 5476 self._view.ui.tabWidget.setCurrentIndex(0) 5477 self._view.ui.tabWidget.setTabEnabled(1, False) 5478 self._view.ui.tabWidget.setTabEnabled(0, True) 5479 tools.switch_page( 5480 self._view.ui.stackedWidget, 5481 self._view.ui.lbl_page_title, 5482 21, 5483 "Monomer Prediction + Analysis", 5484 ) 5485 self.last_sidebar_button = styles.color_sidebar_buttons( 5486 self.last_sidebar_button, 5487 self._view.ui.btn_pred_analysis_monomer_page, 5488 ) 5489 self._view.ui.table_pred_analysis_mono_prot_to_predict.setEnabled(True) 5490 5491 # <editor-fold desc="Sections"> 5492 5493 # <editor-fold desc="Prediction section"> 5494 def mono_pred_analysis_validate_protein_name(self) -> None: 5495 """Validates the input of the protein name in real-time.""" 5496 if safeguard.Safeguard.check_if_value_is_in_table_v_header( 5497 self._view.ui.txt_pred_analysis_mono_prot_name.text(), 5498 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5499 ): 5500 self._view.ui.lbl_pred_analysis_mono_prot_name_status.setText("Protein name already used.") 5501 self._view.ui.btn_pred_analysis_mono_next.setEnabled(False) 5502 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_mono_next) 5503 else: 5504 self._view.ui.btn_pred_analysis_mono_next.setEnabled(True) 5505 tools.validate_protein_name( 5506 self._view.ui.txt_pred_analysis_mono_prot_name, 5507 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5508 self._view.ui.btn_pred_analysis_mono_next, 5509 ) 5510 5511 def mono_pred_analysis_validate_protein_sequence(self) -> None: 5512 """Validates the input of the protein sequence in real-time.""" 5513 tools.validate_protein_sequence( 5514 self._view.ui.txt_pred_analysis_mono_seq_name, 5515 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5516 self._view.ui.btn_pred_analysis_mono_add_protein, 5517 ) 5518 5519 def mono_pred_analysis_check_if_table_is_empty(self) -> None: 5520 """Checks if the table proteins to predict is empty.""" 5521 if self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() == 0: 5522 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_mono_go_analysis_setup) 5523 self._view.ui.btn_pred_analysis_mono_go_analysis_setup.setEnabled(False) 5524 gui_elements_to_show = [ 5525 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5526 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5527 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5528 ] 5529 gui_elements_to_hide = [ 5530 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5531 self._view.ui.lbl_pred_analysis_mono_prot_name, 5532 self._view.ui.txt_pred_analysis_mono_prot_name, 5533 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5534 self._view.ui.btn_pred_analysis_mono_back, 5535 self._view.ui.btn_pred_analysis_mono_next, 5536 self._view.ui.lbl_pred_analysis_mono_seq_name, 5537 self._view.ui.txt_pred_analysis_mono_seq_name, 5538 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5539 self._view.ui.btn_pred_analysis_mono_back_2, 5540 self._view.ui.btn_pred_analysis_mono_add_protein, 5541 self._view.ui.lbl_pred_mono_advanced_config_2, 5542 self._view.ui.btn_pred_mono_advanced_config_2, 5543 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5544 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5545 ] 5546 gui_utils.show_gui_elements(gui_elements_to_show) 5547 gui_utils.hide_gui_elements(gui_elements_to_hide) 5548 else: 5549 gui_elements_to_show = [ 5550 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5551 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5552 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5553 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5554 self._view.ui.lbl_pred_mono_advanced_config_2, 5555 self._view.ui.btn_pred_mono_advanced_config_2, 5556 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5557 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5558 ] 5559 gui_elements_to_hide = [ 5560 self._view.ui.lbl_pred_analysis_mono_prot_name, 5561 self._view.ui.txt_pred_analysis_mono_prot_name, 5562 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5563 self._view.ui.btn_pred_analysis_mono_back, 5564 self._view.ui.btn_pred_analysis_mono_next, 5565 self._view.ui.lbl_pred_analysis_mono_seq_name, 5566 self._view.ui.txt_pred_analysis_mono_seq_name, 5567 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5568 self._view.ui.btn_pred_analysis_mono_back_2, 5569 self._view.ui.btn_pred_analysis_mono_add_protein, 5570 ] 5571 gui_utils.show_gui_elements(gui_elements_to_show) 5572 gui_utils.hide_gui_elements(gui_elements_to_hide) 5573 self._view.ui.btn_pred_analysis_mono_go_analysis_setup.setEnabled(True) 5574 5575 def setup_defaults_monomer_prediction_analysis(self) -> None: 5576 """Sets up default values for the prediction tab.""" 5577 # clears everything 5578 self._view.ui.txt_pred_analysis_mono_prot_name.clear() 5579 self._view.ui.txt_pred_analysis_mono_seq_name.clear() 5580 # sets up defaults: Prediction 5581 self._view.ui.btn_pred_analysis_mono_next.setEnabled(False) 5582 self._view.ui.btn_pred_analysis_mono_add_protein.setEnabled(False) 5583 self._view.ui.lbl_pred_analysis_mono_prot_name_status.setText("") 5584 self._view.ui.lbl_pred_analysis_mono_seq_name_status.setText("") 5585 5586 def mono_pred_analysis_add_seq_to_predict(self) -> None: 5587 """Shows the gui elements for the protein name.""" 5588 gui_elements_to_show = [ 5589 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5590 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5591 self._view.ui.lbl_pred_analysis_mono_prot_name, 5592 self._view.ui.txt_pred_analysis_mono_prot_name, 5593 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5594 self._view.ui.btn_pred_analysis_mono_back, 5595 self._view.ui.btn_pred_analysis_mono_next, 5596 ] 5597 gui_utils.enable_text_box( 5598 self._view.ui.txt_pred_analysis_mono_prot_name, 5599 self._view.ui.lbl_pred_analysis_mono_prot_name, 5600 ) 5601 gui_elements_to_hide = [ 5602 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5603 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5604 self._view.ui.lbl_pred_analysis_mono_seq_name, 5605 self._view.ui.txt_pred_analysis_mono_seq_name, 5606 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5607 self._view.ui.btn_pred_analysis_mono_back_2, 5608 self._view.ui.btn_pred_analysis_mono_add_protein, 5609 self._view.ui.lbl_pred_mono_advanced_config_2, 5610 self._view.ui.btn_pred_mono_advanced_config_2, 5611 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5612 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5613 ] 5614 gui_utils.disable_text_box( 5615 self._view.ui.txt_pred_analysis_mono_seq_name, 5616 self._view.ui.lbl_pred_analysis_mono_seq_name, 5617 ) 5618 gui_utils.show_gui_elements(gui_elements_to_show) 5619 gui_utils.hide_gui_elements(gui_elements_to_hide) 5620 self._view.ui.btn_pred_analysis_mono_next.setEnabled(False) 5621 self._view.ui.txt_pred_analysis_mono_prot_name.clear() 5622 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_mono_next) 5623 if self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() > 0: 5624 try: 5625 self._view.ui.table_pred_analysis_mono_prot_to_predict.currentItem().setSelected(False) 5626 except AttributeError: 5627 constants.PYSSA_LOGGER.debug("No selection on Local Monomer Prediction in overview table.") 5628 5629 def mono_pred_analysis_back(self) -> None: 5630 """Hides the gui elements for the protein name.""" 5631 gui_elements_to_show = [ 5632 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5633 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5634 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5635 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5636 ] 5637 gui_elements_to_hide = [ 5638 self._view.ui.lbl_pred_analysis_mono_prot_name, 5639 self._view.ui.txt_pred_analysis_mono_prot_name, 5640 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5641 self._view.ui.btn_pred_analysis_mono_back, 5642 self._view.ui.btn_pred_analysis_mono_next, 5643 self._view.ui.lbl_pred_analysis_mono_seq_name, 5644 self._view.ui.txt_pred_analysis_mono_seq_name, 5645 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5646 self._view.ui.btn_pred_analysis_mono_back_2, 5647 self._view.ui.btn_pred_analysis_mono_add_protein, 5648 self._view.ui.lbl_pred_mono_advanced_config_2, 5649 self._view.ui.btn_pred_mono_advanced_config_2, 5650 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5651 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5652 ] 5653 gui_utils.show_gui_elements(gui_elements_to_show) 5654 gui_utils.hide_gui_elements(gui_elements_to_hide) 5655 self.mono_pred_analysis_check_if_table_is_empty() 5656 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.setEnabled(False) 5657 5658 def mono_pred_analysis_next(self) -> None: 5659 """Shows the gui elements for the protein sequence.""" 5660 gui_elements_to_show = [ 5661 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5662 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5663 self._view.ui.lbl_pred_analysis_mono_prot_name, 5664 self._view.ui.txt_pred_analysis_mono_prot_name, 5665 self._view.ui.lbl_pred_analysis_mono_seq_name, 5666 self._view.ui.txt_pred_analysis_mono_seq_name, 5667 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5668 self._view.ui.btn_pred_analysis_mono_back_2, 5669 self._view.ui.btn_pred_analysis_mono_add_protein, 5670 ] 5671 gui_utils.enable_text_box( 5672 self._view.ui.txt_pred_analysis_mono_seq_name, 5673 self._view.ui.lbl_pred_analysis_mono_seq_name, 5674 ) 5675 gui_elements_to_hide = [ 5676 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5677 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5678 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5679 self._view.ui.btn_pred_analysis_mono_back, 5680 self._view.ui.btn_pred_analysis_mono_next, 5681 self._view.ui.lbl_pred_mono_advanced_config_2, 5682 self._view.ui.btn_pred_mono_advanced_config_2, 5683 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5684 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5685 ] 5686 gui_utils.disable_text_box( 5687 self._view.ui.txt_pred_analysis_mono_prot_name, 5688 self._view.ui.lbl_pred_analysis_mono_prot_name, 5689 ) 5690 gui_utils.show_gui_elements(gui_elements_to_show) 5691 gui_utils.hide_gui_elements(gui_elements_to_hide) 5692 self._view.ui.txt_pred_analysis_mono_seq_name.clear() 5693 5694 def mono_pred_analysis_back_2(self) -> None: 5695 """Hides the gui elements for the protein sequence.""" 5696 gui_elements_to_show = [ 5697 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5698 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5699 self._view.ui.lbl_pred_analysis_mono_prot_name, 5700 self._view.ui.txt_pred_analysis_mono_prot_name, 5701 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5702 self._view.ui.btn_pred_analysis_mono_back, 5703 self._view.ui.btn_pred_analysis_mono_next, 5704 ] 5705 gui_elements_to_hide = [ 5706 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5707 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5708 self._view.ui.lbl_pred_analysis_mono_seq_name, 5709 self._view.ui.txt_pred_analysis_mono_seq_name, 5710 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5711 self._view.ui.btn_pred_analysis_mono_back_2, 5712 self._view.ui.btn_pred_analysis_mono_add_protein, 5713 self._view.ui.lbl_pred_mono_advanced_config_2, 5714 self._view.ui.btn_pred_mono_advanced_config_2, 5715 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5716 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5717 ] 5718 gui_utils.enable_text_box( 5719 self._view.ui.txt_pred_analysis_mono_prot_name, 5720 self._view.ui.lbl_pred_analysis_mono_prot_name, 5721 ) 5722 gui_utils.disable_text_box( 5723 self._view.ui.txt_pred_analysis_mono_seq_name, 5724 self._view.ui.lbl_pred_analysis_mono_seq_name, 5725 ) 5726 gui_utils.show_gui_elements(gui_elements_to_show) 5727 gui_utils.hide_gui_elements(gui_elements_to_hide) 5728 5729 def mono_pred_analysis_add_protein(self) -> None: 5730 """Adds the protein to the list of proteins to predict.""" 5731 self._view.ui.table_pred_analysis_mono_prot_to_predict.setRowCount( 5732 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() + 1, 5733 ) 5734 self._view.ui.table_pred_analysis_mono_prot_to_predict.insertRow( 5735 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() + 1, 5736 ) 5737 self._view.ui.table_pred_analysis_mono_prot_to_predict.setItem( 5738 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5739 0, 5740 QtWidgets.QTableWidgetItem("A"), 5741 ) 5742 self._view.ui.table_pred_analysis_mono_prot_to_predict.setItem( 5743 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5744 1, 5745 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_analysis_mono_seq_name.toPlainText()), 5746 ) 5747 self._view.ui.table_pred_analysis_mono_prot_to_predict.setVerticalHeaderItem( 5748 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5749 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_analysis_mono_prot_name.text()), 5750 ) 5751 self._view.ui.table_pred_analysis_mono_prot_to_predict.resizeColumnsToContents() 5752 self.mono_pred_analysis_check_if_table_is_empty() 5753 gui_elements_to_show = [ 5754 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5755 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5756 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5757 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5758 self._view.ui.lbl_pred_mono_advanced_config_2, 5759 self._view.ui.btn_pred_mono_advanced_config_2, 5760 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5761 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5762 ] 5763 gui_utils.enable_text_box( 5764 self._view.ui.txt_pred_analysis_mono_prot_name, 5765 self._view.ui.lbl_pred_analysis_mono_prot_name, 5766 ) 5767 gui_elements_to_hide = [ 5768 self._view.ui.lbl_pred_analysis_mono_prot_name, 5769 self._view.ui.txt_pred_analysis_mono_prot_name, 5770 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5771 self._view.ui.btn_pred_analysis_mono_back, 5772 self._view.ui.btn_pred_analysis_mono_next, 5773 self._view.ui.lbl_pred_analysis_mono_seq_name, 5774 self._view.ui.txt_pred_analysis_mono_seq_name, 5775 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5776 self._view.ui.btn_pred_analysis_mono_back_2, 5777 self._view.ui.btn_pred_analysis_mono_add_protein, 5778 ] 5779 gui_utils.show_gui_elements(gui_elements_to_show) 5780 gui_utils.hide_gui_elements(gui_elements_to_hide) 5781 self._view.ui.btn_pred_analysis_mono_go_analysis_setup.setEnabled(True) 5782 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.setEnabled(False) 5783 self.setup_defaults_monomer_prediction() 5784 5785 def mono_pred_analysis_prediction_overview_item_clicked(self) -> None: 5786 """Enables the remove button.""" 5787 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.setEnabled(True) 5788 5789 def mono_pred_analysis_add_protein_to_predict(self) -> None: 5790 """Needs to be removed.""" 5791 self._view.ui.table_pred_analysis_mono_prot_to_predict.setRowCount( 5792 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() + 1, 5793 ) 5794 self._view.ui.table_pred_analysis_mono_prot_to_predict.insertRow( 5795 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() + 1, 5796 ) 5797 self._view.ui.table_pred_analysis_mono_prot_to_predict.setItem( 5798 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5799 0, 5800 QtWidgets.QTableWidgetItem("A"), 5801 ) 5802 self._view.ui.table_pred_analysis_mono_prot_to_predict.setItem( 5803 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5804 1, 5805 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_analysis_mono_seq_name.toPlainText()), 5806 ) 5807 self._view.ui.table_pred_analysis_mono_prot_to_predict.setVerticalHeaderItem( 5808 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5809 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_analysis_mono_prot_name.text()), 5810 ) 5811 self._view.ui.table_pred_analysis_mono_prot_to_predict.resizeColumnsToContents() 5812 self.mono_pred_analysis_check_if_table_is_empty() 5813 self.setup_defaults_monomer_prediction_analysis() 5814 5815 def mono_pred_analysis_remove_protein_to_predict(self) -> None: 5816 """Removes the selected protein from the list of proteins to predict.""" 5817 self._view.ui.table_pred_analysis_mono_prot_to_predict.removeRow( 5818 self._view.ui.table_pred_analysis_mono_prot_to_predict.currentRow(), 5819 ) 5820 self.mono_pred_analysis_check_if_table_is_empty() 5821 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.setEnabled(False) 5822 5823 # </editor-fold> 5824 5825 # <editor-fold desc="Analysis section"> 5826 def mono_pred_analysis_structure_analysis_add(self) -> None: 5827 """Shows the gui elements for the selection of the two proteins.""" 5828 gui_elements_to_show = [ 5829 self._view.ui.lbl_pred_analysis_mono_overview, 5830 self._view.ui.list_pred_analysis_mono_overview, 5831 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 5832 self._view.ui.box_pred_analysis_mono_prot_struct_1, 5833 self._view.ui.lbl_analysis_batch_vs_2, 5834 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 5835 self._view.ui.box_pred_analysis_mono_prot_struct_2, 5836 self._view.ui.btn_pred_analysis_mono_back_3, 5837 self._view.ui.btn_pred_analysis_mono_next_2, 5838 ] 5839 gui_elements_to_hide = [ 5840 self._view.ui.btn_pred_analysis_mono_remove, 5841 self._view.ui.btn_pred_analysis_mono_add, 5842 self._view.ui.lbl_pred_analysis_mono_ref_chains, 5843 self._view.ui.list_pred_analysis_mono_ref_chains, 5844 self._view.ui.btn_pred_analysis_mono_back_4, 5845 self._view.ui.btn_pred_analysis_mono_next_3, 5846 self._view.ui.lbl_pred_analysis_mono_model_chains, 5847 self._view.ui.list_pred_analysis_mono_model_chains, 5848 self._view.ui.btn_pred_analysis_mono_back_5, 5849 self._view.ui.btn_pred_analysis_mono_next_4, 5850 self._view.ui.lbl_pred_analysis_mono_images, 5851 self._view.ui.cb_pred_analysis_mono_images, 5852 self._view.ui.btn_pred_analysis_mono_start, 5853 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 5854 ] 5855 gui_utils.show_gui_elements(gui_elements_to_show) 5856 gui_utils.hide_gui_elements(gui_elements_to_hide) 5857 self._view.ui.lbl_pred_analysis_mono_prot_struct_1.clear() 5858 self._view.ui.lbl_pred_analysis_mono_prot_struct_2.clear() 5859 self._view.ui.lbl_pred_analysis_mono_prot_struct_1.setText("Protein structure 1") 5860 self._view.ui.lbl_pred_analysis_mono_prot_struct_2.setText("Protein structure 2") 5861 self.fill_mono_pred_analysis_protein_boxes() 5862 if self._view.ui.list_pred_analysis_mono_overview.count() > 0: 5863 try: 5864 self._view.ui.list_pred_analysis_mono_overview.currentItem().setSelected(False) 5865 except AttributeError: 5866 constants.PYSSA_LOGGER.debug("No selection in struction analysis overview.") 5867 5868 def mono_pred_analysis_structure_analysis_back_3(self) -> None: 5869 """Hides the gui elements to select the two proteins.""" 5870 gui_elements_to_show = [ 5871 self._view.ui.lbl_pred_analysis_mono_overview, 5872 self._view.ui.list_pred_analysis_mono_overview, 5873 self._view.ui.btn_pred_analysis_mono_add, 5874 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 5875 ] 5876 gui_elements_to_hide = [ 5877 self._view.ui.btn_pred_analysis_mono_remove, 5878 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 5879 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 5880 self._view.ui.lbl_analysis_batch_vs_2, 5881 self._view.ui.lbl_pred_analysis_mono_ref_chains, 5882 self._view.ui.list_pred_analysis_mono_ref_chains, 5883 self._view.ui.btn_pred_analysis_mono_back_4, 5884 self._view.ui.btn_pred_analysis_mono_next_3, 5885 self._view.ui.box_pred_analysis_mono_prot_struct_1, 5886 self._view.ui.box_pred_analysis_mono_prot_struct_2, 5887 self._view.ui.btn_pred_analysis_mono_back_3, 5888 self._view.ui.btn_pred_analysis_mono_next_2, 5889 self._view.ui.lbl_pred_analysis_mono_model_chains, 5890 self._view.ui.list_pred_analysis_mono_model_chains, 5891 self._view.ui.btn_pred_analysis_mono_back_5, 5892 self._view.ui.btn_pred_analysis_mono_next_4, 5893 self._view.ui.lbl_pred_analysis_mono_images, 5894 self._view.ui.cb_pred_analysis_mono_images, 5895 self._view.ui.btn_pred_analysis_mono_start, 5896 ] 5897 gui_utils.show_gui_elements(gui_elements_to_show) 5898 gui_utils.hide_gui_elements(gui_elements_to_hide) 5899 if self._view.ui.list_pred_analysis_mono_overview.count() > 0: 5900 self._view.ui.btn_pred_analysis_mono_remove.show() 5901 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(False) 5902 self._view.ui.btn_pred_analysis_mono_start.show() 5903 self._view.ui.lbl_pred_analysis_mono_images.show() 5904 self._view.ui.cb_pred_analysis_mono_images.show() 5905 5906 def mono_pred_analysis_structure_analysis_next_3(self) -> None: 5907 """Shows the gui elements to select the chains of protein 2.""" 5908 gui_elements_to_show = [ 5909 self._view.ui.lbl_pred_analysis_mono_overview, 5910 self._view.ui.list_pred_analysis_mono_overview, 5911 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 5912 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 5913 self._view.ui.lbl_analysis_batch_vs_2, 5914 self._view.ui.lbl_pred_analysis_mono_ref_chains, 5915 self._view.ui.list_pred_analysis_mono_ref_chains, 5916 self._view.ui.lbl_pred_analysis_mono_model_chains, 5917 self._view.ui.list_pred_analysis_mono_model_chains, 5918 self._view.ui.btn_pred_analysis_mono_back_5, 5919 self._view.ui.btn_pred_analysis_mono_next_4, 5920 ] 5921 gui_elements_to_hide = [ 5922 self._view.ui.btn_pred_analysis_mono_remove, 5923 self._view.ui.btn_pred_analysis_mono_add, 5924 self._view.ui.box_pred_analysis_mono_prot_struct_1, 5925 self._view.ui.box_pred_analysis_mono_prot_struct_2, 5926 self._view.ui.btn_pred_analysis_mono_back_3, 5927 self._view.ui.btn_pred_analysis_mono_next_2, 5928 self._view.ui.btn_pred_analysis_mono_back_4, 5929 self._view.ui.btn_pred_analysis_mono_next_3, 5930 self._view.ui.lbl_pred_analysis_mono_images, 5931 self._view.ui.cb_pred_analysis_mono_images, 5932 self._view.ui.btn_pred_analysis_mono_start, 5933 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 5934 ] 5935 gui_utils.show_gui_elements(gui_elements_to_show) 5936 gui_utils.hide_gui_elements(gui_elements_to_hide) 5937 self._view.ui.list_pred_analysis_mono_model_chains.clear() 5938 self._view.ui.list_pred_analysis_mono_ref_chains.setEnabled(False) 5939 self._view.ui.btn_pred_analysis_mono_next_4.setEnabled(False) 5940 5941 for i in range(self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount()): 5942 if ( 5943 self._view.ui.table_pred_analysis_mono_prot_to_predict.verticalHeaderItem(i).text() 5944 == self._view.ui.box_pred_analysis_mono_prot_struct_2.currentText() 5945 ): 5946 self._view.ui.list_pred_analysis_mono_model_chains.addItem( 5947 self._view.ui.table_pred_analysis_mono_prot_to_predict.item(i, 0).text(), 5948 ) 5949 if self._view.ui.list_pred_analysis_mono_model_chains.count() == 0: 5950 tmp_protein = self._current_project.search_protein( 5951 self._view.ui.box_pred_analysis_mono_prot_struct_2.currentText(), 5952 ) 5953 for tmp_chain in tmp_protein.chains: 5954 if tmp_chain.chain_type == "protein_chain": 5955 self._view.ui.list_pred_analysis_mono_model_chains.addItem(tmp_chain.chain_letter) 5956 if self._view.ui.list_pred_analysis_mono_model_chains.count() == 1: 5957 self._view.ui.lbl_pred_analysis_mono_model_chains.setText( 5958 f"Select chain in protein structure {self._view.ui.lbl_pred_analysis_mono_prot_struct_2.text()}.", 5959 ) 5960 else: 5961 self._view.ui.lbl_pred_analysis_mono_model_chains.setText( 5962 f"Select {len(self._view.ui.list_pred_analysis_mono_model_chains.selectedItems())} chains " 5963 f"in protein structure {self._view.ui.lbl_pred_analysis_mono_prot_struct_2.text()}.", 5964 ) 5965 5966 def mono_pred_analysis_structure_analysis_back_4(self) -> None: 5967 """Hides the gui elements to select the chains in protein 1.""" 5968 gui_elements_to_show = [ 5969 self._view.ui.lbl_pred_analysis_mono_overview, 5970 self._view.ui.list_pred_analysis_mono_overview, 5971 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 5972 self._view.ui.box_pred_analysis_mono_prot_struct_1, 5973 self._view.ui.lbl_analysis_batch_vs_2, 5974 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 5975 self._view.ui.box_pred_analysis_mono_prot_struct_2, 5976 self._view.ui.btn_pred_analysis_mono_back_3, 5977 self._view.ui.btn_pred_analysis_mono_next_2, 5978 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 5979 ] 5980 gui_elements_to_hide = [ 5981 self._view.ui.btn_pred_analysis_mono_remove, 5982 self._view.ui.btn_pred_analysis_mono_add, 5983 self._view.ui.lbl_pred_analysis_mono_ref_chains, 5984 self._view.ui.list_pred_analysis_mono_ref_chains, 5985 self._view.ui.btn_pred_analysis_mono_back_4, 5986 self._view.ui.btn_pred_analysis_mono_next_3, 5987 self._view.ui.lbl_pred_analysis_mono_model_chains, 5988 self._view.ui.list_pred_analysis_mono_model_chains, 5989 self._view.ui.btn_pred_analysis_mono_back_5, 5990 self._view.ui.btn_pred_analysis_mono_next_4, 5991 self._view.ui.lbl_pred_analysis_mono_images, 5992 self._view.ui.cb_pred_analysis_mono_images, 5993 self._view.ui.btn_pred_analysis_mono_start, 5994 ] 5995 gui_utils.show_gui_elements(gui_elements_to_show) 5996 gui_utils.hide_gui_elements(gui_elements_to_hide) 5997 self._view.ui.lbl_pred_analysis_mono_prot_struct_1.setText("Protein structure 1") 5998 self._view.ui.lbl_pred_analysis_mono_prot_struct_2.setText("Protein structure 2") 5999 6000 def mono_pred_analysis_structure_analysis_next_4(self) -> None: 6001 """Adds the protein pair to the list of protein pairs to analyze.""" 6002 gui_elements_to_show = [ 6003 self._view.ui.btn_pred_analysis_mono_remove, 6004 self._view.ui.btn_pred_analysis_mono_add, 6005 self._view.ui.lbl_pred_analysis_mono_overview, 6006 self._view.ui.list_pred_analysis_mono_overview, 6007 self._view.ui.lbl_pred_analysis_mono_images, 6008 self._view.ui.cb_pred_analysis_mono_images, 6009 self._view.ui.btn_pred_analysis_mono_start, 6010 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 6011 ] 6012 gui_elements_to_hide = [ 6013 self._view.ui.box_pred_analysis_mono_prot_struct_1, 6014 self._view.ui.box_pred_analysis_mono_prot_struct_2, 6015 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 6016 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 6017 self._view.ui.lbl_analysis_batch_vs_2, 6018 self._view.ui.lbl_pred_analysis_mono_ref_chains, 6019 self._view.ui.list_pred_analysis_mono_ref_chains, 6020 self._view.ui.lbl_pred_analysis_mono_model_chains, 6021 self._view.ui.list_pred_analysis_mono_model_chains, 6022 self._view.ui.btn_pred_analysis_mono_back_3, 6023 self._view.ui.btn_pred_analysis_mono_next_2, 6024 self._view.ui.btn_pred_analysis_mono_back_4, 6025 self._view.ui.btn_pred_analysis_mono_next_3, 6026 self._view.ui.btn_pred_analysis_mono_back_5, 6027 self._view.ui.btn_pred_analysis_mono_next_4, 6028 ] 6029 gui_utils.show_gui_elements(gui_elements_to_show) 6030 gui_utils.hide_gui_elements(gui_elements_to_hide) 6031 prot_1_name = self._view.ui.lbl_pred_analysis_mono_prot_struct_1.text() 6032 prot_1_chains = [] 6033 for chain in self._view.ui.list_pred_analysis_mono_ref_chains.selectedItems(): 6034 prot_1_chains.append(chain.text()) 6035 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 6036 prot_2_name = self._view.ui.lbl_pred_analysis_mono_prot_struct_2.text() 6037 prot_2_chains = [] 6038 for chain in self._view.ui.list_pred_analysis_mono_model_chains.selectedItems(): 6039 prot_2_chains.append(chain.text()) 6040 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 6041 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 6042 item = QtWidgets.QListWidgetItem(analysis_name) 6043 self._view.ui.list_pred_analysis_mono_overview.addItem(item) 6044 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(False) 6045 6046 def mono_pred_analysis_structure_analysis_back_5(self) -> None: 6047 """Hides the gui elements to select the chains in protein 2.""" 6048 gui_elements_to_show = [ 6049 self._view.ui.lbl_pred_analysis_mono_overview, 6050 self._view.ui.list_pred_analysis_mono_overview, 6051 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 6052 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 6053 self._view.ui.lbl_analysis_batch_vs_2, 6054 self._view.ui.lbl_pred_analysis_mono_ref_chains, 6055 self._view.ui.list_pred_analysis_mono_ref_chains, 6056 self._view.ui.btn_pred_analysis_mono_back_4, 6057 self._view.ui.btn_pred_analysis_mono_next_3, 6058 ] 6059 gui_elements_to_hide = [ 6060 self._view.ui.btn_pred_analysis_mono_remove, 6061 self._view.ui.btn_pred_analysis_mono_add, 6062 self._view.ui.box_pred_analysis_mono_prot_struct_1, 6063 self._view.ui.box_pred_analysis_mono_prot_struct_2, 6064 self._view.ui.btn_pred_analysis_mono_back_3, 6065 self._view.ui.btn_pred_analysis_mono_next_2, 6066 self._view.ui.btn_pred_analysis_mono_back_5, 6067 self._view.ui.btn_pred_analysis_mono_next_4, 6068 self._view.ui.lbl_pred_analysis_mono_images, 6069 self._view.ui.cb_pred_analysis_mono_images, 6070 self._view.ui.btn_pred_analysis_mono_start, 6071 self._view.ui.lbl_pred_analysis_mono_model_chains, 6072 self._view.ui.list_pred_analysis_mono_model_chains, 6073 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 6074 ] 6075 gui_utils.show_gui_elements(gui_elements_to_show) 6076 gui_utils.hide_gui_elements(gui_elements_to_hide) 6077 self._view.ui.list_pred_analysis_mono_ref_chains.setEnabled(True) 6078 6079 # tmp_protein = self._current_project.search_protein(self._view.ui.box_pred_analysis_mono_prot_struct_2.currentText()) 6080 # for tmp_chain in tmp_protein.chains: 6081 # if tmp_chain.chain_type == "protein_chain": 6082 # self._view.ui.list_pred_analysis_mono_ref_chains.addItem(tmp_chain.chain_letter) 6083 6084 def mono_pred_analysis_structure_analysis_overview_clicked(self) -> None: 6085 """Enables the remove button.""" 6086 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(True) 6087 6088 def fill_mono_pred_analysis_protein_boxes(self) -> None: 6089 """Fills the combo box of the protein structures.""" 6090 protein_names = [] 6091 for i in range(self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount()): 6092 protein_names.append(self._view.ui.table_pred_analysis_mono_prot_to_predict.verticalHeaderItem(i).text()) 6093 for tmp_protein in self._current_project.proteins: 6094 protein_names.append(tmp_protein.get_molecule_object()) 6095 protein_names.insert(0, "") 6096 self._view.ui.box_pred_analysis_mono_prot_struct_1.clear() 6097 self._view.ui.box_pred_analysis_mono_prot_struct_2.clear() 6098 gui_utils.fill_combo_box(self._view.ui.box_pred_analysis_mono_prot_struct_1, protein_names) 6099 gui_utils.fill_combo_box(self._view.ui.box_pred_analysis_mono_prot_struct_2, protein_names) 6100 6101 def remove_mono_pred_analysis_analysis_run(self) -> None: 6102 """Removes a selected protein pair form the list of protein pairs to analyze.""" 6103 self._view.ui.list_pred_analysis_mono_overview.takeItem( 6104 self._view.ui.list_pred_analysis_mono_overview.currentRow(), 6105 ) 6106 gui_elements_to_show = [ 6107 self._view.ui.lbl_pred_analysis_mono_overview, 6108 self._view.ui.list_pred_analysis_mono_overview, 6109 self._view.ui.btn_pred_analysis_mono_add, 6110 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 6111 ] 6112 gui_elements_to_hide = [ 6113 self._view.ui.btn_pred_analysis_mono_remove, 6114 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 6115 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 6116 self._view.ui.lbl_analysis_batch_vs_2, 6117 self._view.ui.lbl_pred_analysis_mono_ref_chains, 6118 self._view.ui.list_pred_analysis_mono_ref_chains, 6119 self._view.ui.btn_pred_analysis_mono_back_4, 6120 self._view.ui.btn_pred_analysis_mono_next_3, 6121 self._view.ui.box_pred_analysis_mono_prot_struct_1, 6122 self._view.ui.box_pred_analysis_mono_prot_struct_2, 6123 self._view.ui.btn_pred_analysis_mono_back_3, 6124 self._view.ui.btn_pred_analysis_mono_next_2, 6125 self._view.ui.lbl_pred_analysis_mono_model_chains, 6126 self._view.ui.list_pred_analysis_mono_model_chains, 6127 self._view.ui.btn_pred_analysis_mono_back_5, 6128 self._view.ui.btn_pred_analysis_mono_next_4, 6129 self._view.ui.lbl_pred_analysis_mono_images, 6130 self._view.ui.cb_pred_analysis_mono_images, 6131 self._view.ui.btn_pred_analysis_mono_start, 6132 ] 6133 gui_utils.show_gui_elements(gui_elements_to_show) 6134 gui_utils.hide_gui_elements(gui_elements_to_hide) 6135 if self._view.ui.list_pred_analysis_mono_overview.count() > 0: 6136 self._view.ui.btn_pred_analysis_mono_remove.show() 6137 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(False) 6138 self._view.ui.btn_pred_analysis_mono_start.show() 6139 self._view.ui.lbl_pred_analysis_mono_images.show() 6140 self._view.ui.cb_pred_analysis_mono_images.show() 6141 # if self._view.ui.list_pred_analysis_mono_overview.count() == 0: 6142 # 6143 # self._view.ui.btn_pred_analysis_mono_back_pred_setup.show() 6144 # self._view.ui.btn_pred_analysis_mono_remove.hide() 6145 6146 def check_mono_pred_analysis_if_same_no_of_chains_selected(self) -> None: 6147 """Checks if the same number of chains were selected.""" 6148 self._view.ui.btn_pred_analysis_mono_next_4.setEnabled(False) 6149 if self.no_of_selected_chains == len(self._view.ui.list_pred_analysis_mono_model_chains.selectedItems()): 6150 self._view.ui.btn_pred_analysis_mono_next_4.setEnabled(True) 6151 6152 prot_1_name = self._view.ui.lbl_pred_analysis_mono_prot_struct_1.text() 6153 prot_1_chains = [] 6154 for chain in self._view.ui.list_pred_analysis_mono_ref_chains.selectedItems(): 6155 prot_1_chains.append(chain.text()) 6156 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 6157 prot_2_name = self._view.ui.lbl_pred_analysis_mono_prot_struct_2.text() 6158 prot_2_chains = [] 6159 for chain in self._view.ui.list_pred_analysis_mono_model_chains.selectedItems(): 6160 prot_2_chains.append(chain.text()) 6161 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 6162 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 6163 for tmp_row in range(self._view.ui.list_pred_analysis_mono_overview.count()): 6164 if analysis_name == self._view.ui.list_pred_analysis_mono_overview.item(tmp_row).text(): 6165 self._view.ui.btn_pred_analysis_mono_next_4.setEnabled(False) 6166 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_mono_next_4) 6167 return 6168 6169 def check_mono_pred_analysis_if_prot_structs_are_filled(self) -> None: 6170 """Checks if two proteins were selected.""" 6171 prot_1 = self._view.ui.box_pred_analysis_mono_prot_struct_1.itemText( 6172 self._view.ui.box_pred_analysis_mono_prot_struct_1.currentIndex(), 6173 ) 6174 prot_2 = self._view.ui.box_pred_analysis_mono_prot_struct_2.itemText( 6175 self._view.ui.box_pred_analysis_mono_prot_struct_2.currentIndex(), 6176 ) 6177 if prot_1 != "" and prot_2 != "": 6178 self._view.ui.btn_pred_analysis_mono_next_2.setEnabled(True) 6179 else: 6180 self._view.ui.btn_pred_analysis_mono_next_2.setEnabled(False) 6181 6182 def count_mono_pred_analysis_selected_chains_for_prot_struct_1(self) -> None: 6183 """Counts the number of chains selected in protein 1.""" 6184 self.no_of_selected_chains = len(self._view.ui.list_pred_analysis_mono_ref_chains.selectedItems()) 6185 if self.no_of_selected_chains > 0: 6186 self._view.ui.btn_pred_analysis_mono_next_3.setEnabled(True) 6187 else: 6188 self._view.ui.btn_pred_analysis_mono_next_3.setEnabled(False) 6189 6190 # </editor-fold> 6191 6192 # </editor-fold> 6193 6194 def switch_monomer_pred_analysis_tab(self) -> None: 6195 """Switches the tabs from prediction to analysis and vice versa.""" 6196 if self._view.ui.tabWidget.currentIndex() == 0: 6197 # goes from prediction to analysis 6198 self._view.ui.tabWidget.setTabEnabled(1, True) 6199 self._view.ui.tabWidget.setTabEnabled(0, False) 6200 self._view.ui.tabWidget.setCurrentIndex(1) 6201 gui_elements_to_show = [ 6202 self._view.ui.lbl_pred_analysis_mono_overview, 6203 self._view.ui.list_pred_analysis_mono_overview, 6204 self._view.ui.btn_pred_analysis_mono_add, 6205 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 6206 ] 6207 gui_elements_to_hide = [ 6208 self._view.ui.btn_pred_analysis_mono_remove, 6209 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 6210 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 6211 self._view.ui.lbl_analysis_batch_vs_2, 6212 self._view.ui.lbl_pred_analysis_mono_ref_chains, 6213 self._view.ui.list_pred_analysis_mono_ref_chains, 6214 self._view.ui.btn_pred_analysis_mono_back_4, 6215 self._view.ui.btn_pred_analysis_mono_next_3, 6216 self._view.ui.box_pred_analysis_mono_prot_struct_1, 6217 self._view.ui.box_pred_analysis_mono_prot_struct_2, 6218 self._view.ui.btn_pred_analysis_mono_back_3, 6219 self._view.ui.btn_pred_analysis_mono_next_2, 6220 self._view.ui.lbl_pred_analysis_mono_model_chains, 6221 self._view.ui.list_pred_analysis_mono_model_chains, 6222 self._view.ui.btn_pred_analysis_mono_back_5, 6223 self._view.ui.btn_pred_analysis_mono_next_4, 6224 self._view.ui.lbl_pred_analysis_mono_images, 6225 self._view.ui.cb_pred_analysis_mono_images, 6226 self._view.ui.btn_pred_analysis_mono_start, 6227 ] 6228 gui_utils.show_gui_elements(gui_elements_to_show) 6229 gui_utils.hide_gui_elements(gui_elements_to_hide) 6230 if self._view.ui.list_pred_analysis_mono_overview.count() > 0: 6231 self._view.ui.btn_pred_analysis_mono_remove.show() 6232 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(False) 6233 self._view.ui.btn_pred_analysis_mono_start.show() 6234 self._view.ui.lbl_pred_analysis_mono_images.show() 6235 self._view.ui.cb_pred_analysis_mono_images.show() 6236 else: 6237 # goes from analysis to prediction 6238 if self._view.ui.list_pred_analysis_mono_overview.count() > 0: 6239 gui_elements_to_show = [ 6240 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 6241 self._view.ui.table_pred_analysis_mono_prot_to_predict, 6242 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 6243 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 6244 ] 6245 gui_elements_to_hide = [ 6246 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 6247 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 6248 self._view.ui.lbl_pred_analysis_mono_prot_name, 6249 self._view.ui.txt_pred_analysis_mono_prot_name, 6250 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 6251 self._view.ui.btn_pred_analysis_mono_back, 6252 self._view.ui.btn_pred_analysis_mono_next, 6253 self._view.ui.lbl_pred_analysis_mono_seq_name, 6254 self._view.ui.txt_pred_analysis_mono_seq_name, 6255 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 6256 self._view.ui.btn_pred_analysis_mono_back_2, 6257 self._view.ui.btn_pred_analysis_mono_add_protein, 6258 self._view.ui.lbl_pred_mono_advanced_config_2, 6259 self._view.ui.btn_pred_mono_advanced_config_2, 6260 ] 6261 gui_utils.show_gui_elements(gui_elements_to_show) 6262 gui_utils.hide_gui_elements(gui_elements_to_hide) 6263 else: 6264 gui_elements_to_show = [ 6265 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 6266 self._view.ui.table_pred_analysis_mono_prot_to_predict, 6267 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 6268 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 6269 self._view.ui.lbl_pred_mono_advanced_config_2, 6270 self._view.ui.btn_pred_mono_advanced_config_2, 6271 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 6272 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 6273 ] 6274 gui_elements_to_hide = [ 6275 self._view.ui.lbl_pred_analysis_mono_prot_name, 6276 self._view.ui.txt_pred_analysis_mono_prot_name, 6277 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 6278 self._view.ui.btn_pred_analysis_mono_back, 6279 self._view.ui.btn_pred_analysis_mono_next, 6280 self._view.ui.lbl_pred_analysis_mono_seq_name, 6281 self._view.ui.txt_pred_analysis_mono_seq_name, 6282 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 6283 self._view.ui.btn_pred_analysis_mono_back_2, 6284 self._view.ui.btn_pred_analysis_mono_add_protein, 6285 ] 6286 gui_utils.show_gui_elements(gui_elements_to_show) 6287 gui_utils.hide_gui_elements(gui_elements_to_hide) 6288 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.setEnabled(False) 6289 self._view.ui.tabWidget.setTabEnabled(0, True) 6290 self._view.ui.tabWidget.setTabEnabled(1, False) 6291 self._view.ui.tabWidget.setCurrentIndex(0) 6292 6293 # </editor-fold> 6294 6295 # <editor-fold desc="Multimer prediction + analysis"> 6296 def _init_multi_pred_analysis_page(self) -> None: 6297 """Clears the text boxes and sets the default values for the gui elements.""" 6298 # <editor-fold desc="Prediction section"> 6299 # clears everything 6300 self._view.ui.txt_pred_analysis_multi_prot_name.clear() 6301 self._view.ui.txt_pred_analysis_multi_prot_seq.clear() 6302 self._view.ui.list_pred_analysis_multi_prot_seq_overview.clear() 6303 for i in range(self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() - 1, -1, -1): 6304 self._view.ui.table_pred_analysis_multi_prot_to_predict.removeRow(i) 6305 6306 # sets up defaults: Prediction 6307 self._view.ui.btn_pred_analysis_multi_next.setEnabled(False) 6308 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2.setEnabled(False) 6309 self._view.ui.lbl_pred_analysis_multi_prot_name_status.setText("") 6310 self._view.ui.lbl_pred_analysis_multi_prot_seq_status.setText("") 6311 6312 # </editor-fold> 6313 6314 # <editor-fold desc="Analysis section"> 6315 self._view.ui.list_pred_analysis_multi_overview.clear() 6316 self._view.ui.btn_pred_analysis_multi_remove.hide() 6317 6318 # </editor-fold> 6319 6320 # self.multi_pred_analysis_show_protein_overview() 6321 6322 def display_multimer_pred_analysis(self) -> None: 6323 """Displays the multimer prediction + analysis page.""" 6324 # checks internet connection 6325 if not tools.check_internet_connectivity(): 6326 gui_utils.no_internet_dialog() 6327 return 6328 6329 self._init_multi_pred_analysis_page() 6330 self._view.ui.table_pred_analysis_multi_prot_to_predict.clear() 6331 self._view.ui.table_pred_analysis_multi_prot_to_predict.setHorizontalHeaderItem( 6332 0, 6333 QtWidgets.QTableWidgetItem("Chain"), 6334 ) 6335 self._view.ui.table_pred_analysis_multi_prot_to_predict.setHorizontalHeaderItem( 6336 1, 6337 QtWidgets.QTableWidgetItem("Sequence"), 6338 ) 6339 self._view.ui.table_pred_analysis_multi_prot_to_predict.resizeColumnsToContents() 6340 gui_elements_to_show = [ 6341 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6342 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6343 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6344 ] 6345 gui_elements_to_hide = [ 6346 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6347 self._view.ui.lbl_pred_analysis_multi_prot_name, 6348 self._view.ui.txt_pred_analysis_multi_prot_name, 6349 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6350 self._view.ui.btn_pred_analysis_multi_back, 6351 self._view.ui.btn_pred_analysis_multi_next, 6352 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6353 self._view.ui.txt_pred_analysis_multi_prot_seq, 6354 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6355 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6356 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6357 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6358 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6359 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6360 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6361 self._view.ui.btn_pred_analysis_multi_back_2, 6362 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6363 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6364 self._view.ui.btn_pred_analysis_multi_advanced_config, 6365 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6366 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6367 ] 6368 gui_utils.show_gui_elements(gui_elements_to_show) 6369 gui_utils.hide_gui_elements(gui_elements_to_hide) 6370 if self._view.ui.tabWidget_2.currentIndex() == 1: 6371 self._view.ui.tabWidget_2.setCurrentIndex(0) 6372 self._view.ui.tabWidget_2.setTabEnabled(1, False) 6373 self._view.ui.tabWidget_2.setTabEnabled(0, True) 6374 tools.switch_page( 6375 self._view.ui.stackedWidget, 6376 self._view.ui.lbl_page_title, 6377 22, 6378 "Multimer Prediction + Analysis", 6379 ) 6380 self.last_sidebar_button = styles.color_sidebar_buttons( 6381 self.last_sidebar_button, 6382 self._view.ui.btn_pred_analysis_multimer_page, 6383 ) 6384 self._view.ui.table_pred_analysis_multi_prot_to_predict.setEnabled(True) 6385 6386 # <editor-fold desc="Prediction section"> 6387 def multi_pred_analysis_validate_protein_name(self) -> None: 6388 """Validates the input of the protein name in real-time.""" 6389 if safeguard.Safeguard.check_if_value_is_in_table_v_header( 6390 self._view.ui.txt_pred_analysis_multi_prot_name.text(), 6391 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6392 ): 6393 self._view.ui.lbl_pred_analysis_multi_prot_name_status.setText("Protein name already used.") 6394 self._view.ui.btn_pred_analysis_multi_next.setEnabled(False) 6395 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_multi_next) 6396 else: 6397 self._view.ui.btn_pred_analysis_multi_next.setEnabled(True) 6398 tools.validate_protein_name( 6399 self._view.ui.txt_pred_analysis_multi_prot_name, 6400 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6401 self._view.ui.btn_pred_analysis_multi_next, 6402 ) 6403 6404 def multi_pred_analysis_validate_protein_sequence(self) -> None: 6405 """Validates the input of the protein sequence in real-time.""" 6406 tools.validate_protein_sequence( 6407 self._view.ui.txt_pred_analysis_multi_prot_seq, 6408 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6409 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6410 ) 6411 6412 def multi_pred_analysis_check_if_list_is_empty(self) -> None: 6413 """Checks if the list of sequences of the protein is empty.""" 6414 if self._view.ui.list_pred_analysis_multi_prot_seq_overview.count() == 0: 6415 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2.setEnabled(False) 6416 else: 6417 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2.setEnabled(True) 6418 6419 def multi_pred_analysis_add_sequence_to_list(self) -> None: 6420 """Adds the entered sequence to the sequences of the protein.""" 6421 self._view.ui.list_pred_analysis_multi_prot_seq_overview.addItem( 6422 QtWidgets.QListWidgetItem(self._view.ui.txt_pred_analysis_multi_prot_seq.toPlainText()), 6423 ) 6424 self.multi_pred_analysis_check_if_list_is_empty() 6425 6426 def multi_pred_analysis_remove_sequence_to_list(self) -> None: 6427 """Removes the entered sequence from the sequences of the protein.""" 6428 self._view.ui.list_pred_analysis_multi_prot_seq_overview.takeItem( 6429 self._view.ui.list_pred_analysis_multi_prot_seq_overview.currentRow(), 6430 ) 6431 self.multi_pred_analysis_check_if_list_is_empty() 6432 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove.setEnabled(False) 6433 6434 def multi_pred_analysis_check_if_table_is_empty(self) -> None: 6435 """Checks if the list of proteins to predict is empty.""" 6436 if self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() == 0: 6437 styles.color_button_not_ready(self._view.ui.btn_pred_multi_predict) 6438 gui_elements_to_show = [ 6439 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6440 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6441 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6442 ] 6443 gui_elements_to_hide = [ 6444 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6445 self._view.ui.lbl_pred_analysis_multi_prot_name, 6446 self._view.ui.txt_pred_analysis_multi_prot_name, 6447 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6448 self._view.ui.btn_pred_analysis_multi_back, 6449 self._view.ui.btn_pred_analysis_multi_next, 6450 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6451 self._view.ui.txt_pred_analysis_multi_prot_seq, 6452 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6453 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6454 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6455 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6456 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6457 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6458 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6459 self._view.ui.btn_pred_analysis_multi_back_2, 6460 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6461 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6462 self._view.ui.btn_pred_analysis_multi_advanced_config, 6463 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6464 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6465 ] 6466 gui_utils.show_gui_elements(gui_elements_to_show) 6467 gui_utils.hide_gui_elements(gui_elements_to_hide) 6468 self._view.ui.btn_pred_multi_predict.setEnabled(False) 6469 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False) 6470 else: 6471 self._view.ui.btn_pred_multi_predict.setEnabled(True) 6472 gui_elements_to_show = [ 6473 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6474 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6475 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6476 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6477 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6478 self._view.ui.btn_pred_analysis_multi_advanced_config, 6479 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6480 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6481 ] 6482 gui_elements_to_hide = [ 6483 self._view.ui.lbl_pred_analysis_multi_prot_name, 6484 self._view.ui.txt_pred_analysis_multi_prot_name, 6485 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6486 self._view.ui.btn_pred_analysis_multi_back, 6487 self._view.ui.btn_pred_analysis_multi_next, 6488 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6489 self._view.ui.txt_pred_analysis_multi_prot_seq, 6490 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6491 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6492 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6493 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6494 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6495 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6496 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6497 self._view.ui.btn_pred_analysis_multi_back_2, 6498 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6499 ] 6500 gui_utils.show_gui_elements(gui_elements_to_show) 6501 gui_utils.hide_gui_elements(gui_elements_to_hide) 6502 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False) 6503 6504 def multi_pred_analysis_add_protein_to_predict(self) -> None: 6505 """Adds the proteins to the list of proteins to predict.""" 6506 for i in range(self._view.ui.list_pred_analysis_multi_prot_seq_overview.count()): 6507 self._view.ui.table_pred_analysis_multi_prot_to_predict.setRowCount( 6508 self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() + 1, 6509 ) 6510 self._view.ui.table_pred_analysis_multi_prot_to_predict.insertRow( 6511 self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() + 1, 6512 ) 6513 tmp_chain_seq = ( 6514 constants.chain_dict.get(i), 6515 self._view.ui.list_pred_analysis_multi_prot_seq_overview.item(i).text(), 6516 ) 6517 self._view.ui.table_pred_analysis_multi_prot_to_predict.setItem( 6518 self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() - 1, 6519 0, 6520 QtWidgets.QTableWidgetItem(tmp_chain_seq[0]), 6521 ) 6522 self._view.ui.table_pred_analysis_multi_prot_to_predict.setItem( 6523 self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() - 1, 6524 1, 6525 QtWidgets.QTableWidgetItem(tmp_chain_seq[1]), 6526 ) 6527 name_item = QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_analysis_multi_prot_name.text()) 6528 self._view.ui.table_pred_analysis_multi_prot_to_predict.setVerticalHeaderItem( 6529 self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() - 1, 6530 name_item, 6531 ) 6532 self._view.ui.table_pred_analysis_multi_prot_to_predict.resizeColumnsToContents() 6533 self.multi_pred_analysis_check_if_table_is_empty() 6534 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove.setEnabled(False) 6535 6536 def multi_pred_analysis_remove_protein_to_predict(self) -> None: 6537 """Removes the selected protein from the list of proteins to predict.""" 6538 if self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() == 1: 6539 self._view.ui.table_pred_analysis_multi_prot_to_predict.removeRow(0) 6540 else: 6541 self._view.ui.table_pred_analysis_multi_prot_to_predict.removeRow( 6542 self._view.ui.table_pred_analysis_multi_prot_to_predict.currentRow(), 6543 ) 6544 prot_name = self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem( 6545 self._view.ui.table_pred_analysis_multi_prot_to_predict.currentRow(), 6546 ).text() 6547 for i in range(self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount()): 6548 if self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem(i).text() == prot_name: 6549 self._view.ui.table_pred_analysis_multi_prot_to_predict.setItem( 6550 i, 6551 0, 6552 QtWidgets.QTableWidgetItem(constants.chain_dict.get(i)), 6553 ) 6554 self.multi_pred_analysis_check_if_table_is_empty() 6555 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove.setEnabled(False) 6556 6557 def multi_pred_analysis_add(self) -> None: 6558 """Shows the gui elements for the protein name.""" 6559 gui_elements_to_show = [ 6560 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6561 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6562 self._view.ui.lbl_pred_analysis_multi_prot_name, 6563 self._view.ui.txt_pred_analysis_multi_prot_name, 6564 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6565 self._view.ui.btn_pred_analysis_multi_back, 6566 self._view.ui.btn_pred_analysis_multi_next, 6567 ] 6568 gui_elements_to_hide = [ 6569 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6570 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6571 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6572 self._view.ui.txt_pred_analysis_multi_prot_seq, 6573 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6574 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6575 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6576 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6577 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6578 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6579 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6580 self._view.ui.btn_pred_analysis_multi_back_2, 6581 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6582 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6583 self._view.ui.btn_pred_analysis_multi_advanced_config, 6584 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6585 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6586 ] 6587 gui_utils.show_gui_elements(gui_elements_to_show) 6588 gui_utils.hide_gui_elements(gui_elements_to_hide) 6589 gui_utils.enable_text_box( 6590 self._view.ui.txt_pred_analysis_multi_prot_name, 6591 self._view.ui.lbl_pred_analysis_multi_prot_name, 6592 ) 6593 gui_utils.disable_text_box( 6594 self._view.ui.txt_pred_analysis_multi_prot_seq, 6595 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6596 ) 6597 self._view.ui.btn_pred_analysis_multi_next.setEnabled(False) 6598 self._view.ui.txt_pred_analysis_multi_prot_name.clear() 6599 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_multi_next) 6600 if self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() > 0: 6601 try: 6602 self._view.ui.table_pred_analysis_multi_prot_to_predict.currentItem().setSelected(False) 6603 except AttributeError: 6604 constants.PYSSA_LOGGER.debug("No selection on Local Multimer Prediction in overview table.") 6605 6606 def multi_pred_analysis_back(self) -> None: 6607 """Hides the gui elements for the protein name.""" 6608 gui_elements_to_show = [ 6609 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6610 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6611 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6612 ] 6613 gui_elements_to_hide = [ 6614 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6615 self._view.ui.lbl_pred_analysis_multi_prot_name, 6616 self._view.ui.txt_pred_analysis_multi_prot_name, 6617 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6618 self._view.ui.btn_pred_analysis_multi_back, 6619 self._view.ui.btn_pred_analysis_multi_next, 6620 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6621 self._view.ui.txt_pred_analysis_multi_prot_seq, 6622 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6623 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6624 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6625 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6626 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6627 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6628 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6629 self._view.ui.btn_pred_analysis_multi_back_2, 6630 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6631 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6632 self._view.ui.btn_pred_analysis_multi_advanced_config, 6633 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6634 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6635 ] 6636 gui_utils.show_gui_elements(gui_elements_to_show) 6637 gui_utils.hide_gui_elements(gui_elements_to_hide) 6638 self.multi_pred_analysis_check_if_table_is_empty() 6639 6640 def multi_pred_analysis_next(self) -> None: 6641 """Shows the gui elements for the protein sequence.""" 6642 gui_elements_to_show = [ 6643 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6644 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6645 self._view.ui.lbl_pred_analysis_multi_prot_name, 6646 self._view.ui.txt_pred_analysis_multi_prot_name, 6647 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6648 self._view.ui.txt_pred_analysis_multi_prot_seq, 6649 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6650 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6651 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6652 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6653 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6654 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6655 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6656 self._view.ui.btn_pred_analysis_multi_back_2, 6657 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6658 ] 6659 gui_elements_to_hide = [ 6660 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6661 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6662 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6663 self._view.ui.btn_pred_analysis_multi_back, 6664 self._view.ui.btn_pred_analysis_multi_next, 6665 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6666 self._view.ui.btn_pred_analysis_multi_advanced_config, 6667 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6668 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6669 ] 6670 gui_utils.show_gui_elements(gui_elements_to_show) 6671 gui_utils.hide_gui_elements(gui_elements_to_hide) 6672 gui_utils.enable_text_box( 6673 self._view.ui.txt_pred_analysis_multi_prot_seq, 6674 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6675 ) 6676 gui_utils.disable_text_box( 6677 self._view.ui.txt_pred_analysis_multi_prot_name, 6678 self._view.ui.lbl_pred_analysis_multi_prot_name, 6679 ) 6680 self._view.ui.txt_pred_analysis_multi_prot_seq.clear() 6681 self._view.ui.list_pred_analysis_multi_prot_seq_overview.clear() 6682 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2.setEnabled(False) 6683 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove.setEnabled(False) 6684 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2) 6685 6686 def multi_pred_analysis_back_2(self) -> None: 6687 """Hides the gui elements for the protein sequence.""" 6688 gui_elements_to_show = [ 6689 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6690 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6691 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6692 self._view.ui.btn_pred_analysis_multi_back, 6693 self._view.ui.btn_pred_analysis_multi_next, 6694 self._view.ui.lbl_pred_analysis_multi_prot_name, 6695 self._view.ui.txt_pred_analysis_multi_prot_name, 6696 ] 6697 gui_elements_to_hide = [ 6698 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6699 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6700 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6701 self._view.ui.txt_pred_analysis_multi_prot_seq, 6702 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6703 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6704 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6705 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6706 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6707 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6708 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6709 self._view.ui.btn_pred_analysis_multi_back_2, 6710 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6711 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6712 self._view.ui.btn_pred_analysis_multi_advanced_config, 6713 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6714 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6715 ] 6716 gui_utils.show_gui_elements(gui_elements_to_show) 6717 gui_utils.hide_gui_elements(gui_elements_to_hide) 6718 gui_utils.enable_text_box( 6719 self._view.ui.txt_pred_analysis_multi_prot_name, 6720 self._view.ui.lbl_pred_analysis_multi_prot_name, 6721 ) 6722 gui_utils.disable_text_box( 6723 self._view.ui.txt_pred_analysis_multi_prot_seq, 6724 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6725 ) 6726 6727 def multi_pred_analysis_prot_seq_overview_item_changed(self) -> None: 6728 """Enables the remove button of the list of sequences of the protein.""" 6729 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove.setEnabled(True) 6730 6731 def multi_pred_analysis_prot_to_predict_item_changed(self) -> None: 6732 """Enables the remove button of the list of proteins to predict.""" 6733 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove.setEnabled(True) 6734 6735 # </editor-fold> 6736 6737 def switch_multimer_pred_analysis_tab(self) -> None: 6738 """Switches the tabs from prediction to analysis and vice versa.""" 6739 if self._view.ui.tabWidget_2.currentIndex() == 0: 6740 # goes from prediction to analysis 6741 self._view.ui.tabWidget_2.setCurrentIndex(1) 6742 gui_elements_to_show = [ 6743 self._view.ui.lbl_pred_analysis_multi_overview, 6744 self._view.ui.list_pred_analysis_multi_overview, 6745 self._view.ui.btn_pred_analysis_multi_add, 6746 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 6747 ] 6748 gui_elements_to_hide = [ 6749 self._view.ui.btn_pred_analysis_multi_remove, 6750 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 6751 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 6752 self._view.ui.lbl_analysis_batch_vs_3, 6753 self._view.ui.lbl_pred_analysis_multi_ref_chains, 6754 self._view.ui.list_pred_analysis_multi_ref_chains, 6755 self._view.ui.btn_pred_analysis_multi_back_4, 6756 self._view.ui.btn_pred_analysis_multi_next_3, 6757 self._view.ui.box_pred_analysis_multi_prot_struct_1, 6758 self._view.ui.box_pred_analysis_multi_prot_struct_2, 6759 self._view.ui.btn_pred_analysis_multi_back_3, 6760 self._view.ui.btn_pred_analysis_multi_next_2, 6761 self._view.ui.lbl_pred_analysis_multi_model_chains, 6762 self._view.ui.list_pred_analysis_multi_model_chains, 6763 self._view.ui.btn_pred_analysis_multi_back_5, 6764 self._view.ui.btn_pred_analysis_multi_next_4, 6765 self._view.ui.lbl_pred_analysis_multi_images, 6766 self._view.ui.cb_pred_analysis_multi_images, 6767 self._view.ui.btn_pred_analysis_multi_start, 6768 ] 6769 gui_utils.show_gui_elements(gui_elements_to_show) 6770 gui_utils.hide_gui_elements(gui_elements_to_hide) 6771 self._view.ui.tabWidget_2.setTabEnabled(1, True) 6772 self._view.ui.tabWidget_2.setTabEnabled(0, False) 6773 if self._view.ui.list_pred_analysis_multi_overview.count() > 0: 6774 self._view.ui.btn_pred_analysis_multi_remove.show() 6775 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(False) 6776 self._view.ui.btn_pred_analysis_multi_start.show() 6777 self._view.ui.lbl_pred_analysis_multi_images.show() 6778 self._view.ui.cb_pred_analysis_multi_images.show() 6779 else: 6780 # goes from analysis to prediction 6781 self._view.ui.tabWidget_2.setCurrentIndex(0) 6782 if self._view.ui.list_pred_analysis_multi_overview.count() > 0: 6783 gui_elements_to_show = [ 6784 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6785 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6786 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6787 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6788 ] 6789 gui_elements_to_hide = [ 6790 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6791 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6792 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6793 self._view.ui.btn_pred_analysis_multi_advanced_config, 6794 self._view.ui.lbl_pred_analysis_multi_prot_name, 6795 self._view.ui.txt_pred_analysis_multi_prot_name, 6796 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6797 self._view.ui.btn_pred_analysis_multi_back, 6798 self._view.ui.btn_pred_analysis_multi_next, 6799 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6800 self._view.ui.txt_pred_analysis_multi_prot_seq, 6801 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6802 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6803 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6804 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6805 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6806 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6807 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6808 self._view.ui.btn_pred_analysis_multi_back_2, 6809 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6810 ] 6811 gui_utils.show_gui_elements(gui_elements_to_show) 6812 gui_utils.hide_gui_elements(gui_elements_to_hide) 6813 else: 6814 gui_elements_to_show = [ 6815 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6816 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6817 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6818 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6819 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6820 self._view.ui.btn_pred_analysis_multi_advanced_config, 6821 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6822 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6823 ] 6824 gui_elements_to_hide = [ 6825 self._view.ui.lbl_pred_analysis_multi_prot_name, 6826 self._view.ui.txt_pred_analysis_multi_prot_name, 6827 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6828 self._view.ui.btn_pred_analysis_multi_back, 6829 self._view.ui.btn_pred_analysis_multi_next, 6830 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6831 self._view.ui.txt_pred_analysis_multi_prot_seq, 6832 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6833 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6834 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6835 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6836 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6837 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6838 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6839 self._view.ui.btn_pred_analysis_multi_back_2, 6840 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6841 ] 6842 gui_utils.show_gui_elements(gui_elements_to_show) 6843 gui_utils.hide_gui_elements(gui_elements_to_hide) 6844 self._view.ui.tabWidget_2.setTabEnabled(0, True) 6845 self._view.ui.tabWidget_2.setTabEnabled(1, False) 6846 6847 # <editor-fold desc="Analysis section"> 6848 def multi_pred_analysis_structure_analysis_add(self) -> None: 6849 """Shows the gui elements to choose the two proteins.""" 6850 gui_elements_to_show = [ 6851 self._view.ui.lbl_pred_analysis_multi_overview, 6852 self._view.ui.list_pred_analysis_multi_overview, 6853 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 6854 self._view.ui.box_pred_analysis_multi_prot_struct_1, 6855 self._view.ui.lbl_analysis_batch_vs_3, 6856 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 6857 self._view.ui.box_pred_analysis_multi_prot_struct_2, 6858 self._view.ui.btn_pred_analysis_multi_back_3, 6859 self._view.ui.btn_pred_analysis_multi_next_2, 6860 ] 6861 gui_elements_to_hide = [ 6862 self._view.ui.btn_pred_analysis_multi_remove, 6863 self._view.ui.btn_pred_analysis_multi_add, 6864 self._view.ui.lbl_pred_analysis_multi_ref_chains, 6865 self._view.ui.list_pred_analysis_multi_ref_chains, 6866 self._view.ui.btn_pred_analysis_multi_back_4, 6867 self._view.ui.btn_pred_analysis_multi_next_3, 6868 self._view.ui.lbl_pred_analysis_multi_model_chains, 6869 self._view.ui.list_pred_analysis_multi_model_chains, 6870 self._view.ui.btn_pred_analysis_multi_back_5, 6871 self._view.ui.btn_pred_analysis_multi_next_4, 6872 self._view.ui.lbl_pred_analysis_multi_images, 6873 self._view.ui.cb_pred_analysis_multi_images, 6874 self._view.ui.btn_pred_analysis_multi_start, 6875 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 6876 ] 6877 gui_utils.show_gui_elements(gui_elements_to_show) 6878 gui_utils.hide_gui_elements(gui_elements_to_hide) 6879 self._view.ui.lbl_pred_analysis_multi_prot_struct_1.clear() 6880 self._view.ui.lbl_pred_analysis_multi_prot_struct_2.clear() 6881 self._view.ui.lbl_pred_analysis_multi_prot_struct_1.setText("Protein structure 1") 6882 self._view.ui.lbl_pred_analysis_multi_prot_struct_2.setText("Protein structure 2") 6883 self.fill_multi_pred_analysis_protein_boxes() 6884 if self._view.ui.list_pred_analysis_multi_overview.count() > 0: 6885 try: 6886 self._view.ui.list_pred_analysis_multi_overview.currentItem().setSelected(False) 6887 except AttributeError: 6888 constants.PYSSA_LOGGER.debug("No selection in struction analysis overview.") 6889 6890 def multi_pred_analysis_structure_analysis_back_3(self) -> None: 6891 """Hides the gui elements to choose the two proteins.""" 6892 gui_elements_to_show = [ 6893 self._view.ui.lbl_pred_analysis_multi_overview, 6894 self._view.ui.list_pred_analysis_multi_overview, 6895 self._view.ui.btn_pred_analysis_multi_add, 6896 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 6897 ] 6898 gui_elements_to_hide = [ 6899 self._view.ui.btn_pred_analysis_multi_remove, 6900 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 6901 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 6902 self._view.ui.lbl_analysis_batch_vs_3, 6903 self._view.ui.lbl_pred_analysis_multi_ref_chains, 6904 self._view.ui.list_pred_analysis_multi_ref_chains, 6905 self._view.ui.btn_pred_analysis_multi_back_4, 6906 self._view.ui.btn_pred_analysis_multi_next_3, 6907 self._view.ui.box_pred_analysis_multi_prot_struct_1, 6908 self._view.ui.box_pred_analysis_multi_prot_struct_2, 6909 self._view.ui.btn_pred_analysis_multi_back_3, 6910 self._view.ui.btn_pred_analysis_multi_next_2, 6911 self._view.ui.lbl_pred_analysis_multi_model_chains, 6912 self._view.ui.list_pred_analysis_multi_model_chains, 6913 self._view.ui.btn_pred_analysis_multi_back_5, 6914 self._view.ui.btn_pred_analysis_multi_next_4, 6915 self._view.ui.lbl_pred_analysis_multi_images, 6916 self._view.ui.cb_pred_analysis_multi_images, 6917 self._view.ui.btn_pred_analysis_multi_start, 6918 ] 6919 gui_utils.show_gui_elements(gui_elements_to_show) 6920 gui_utils.hide_gui_elements(gui_elements_to_hide) 6921 if self._view.ui.list_pred_analysis_multi_overview.count() > 0: 6922 self._view.ui.btn_pred_analysis_multi_remove.show() 6923 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(False) 6924 self._view.ui.btn_pred_analysis_multi_start.show() 6925 self._view.ui.lbl_pred_analysis_multi_images.show() 6926 self._view.ui.cb_pred_analysis_multi_images.show() 6927 6928 def multi_pred_analysis_structure_analysis_next_3(self) -> None: 6929 """Shows the gui elements to select the chains in protein 2.""" 6930 gui_elements_to_show = [ 6931 self._view.ui.lbl_pred_analysis_multi_overview, 6932 self._view.ui.list_pred_analysis_multi_overview, 6933 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 6934 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 6935 self._view.ui.lbl_analysis_batch_vs_3, 6936 self._view.ui.lbl_pred_analysis_multi_ref_chains, 6937 self._view.ui.list_pred_analysis_multi_ref_chains, 6938 self._view.ui.lbl_pred_analysis_multi_model_chains, 6939 self._view.ui.list_pred_analysis_multi_model_chains, 6940 self._view.ui.btn_pred_analysis_multi_back_5, 6941 self._view.ui.btn_pred_analysis_multi_next_4, 6942 ] 6943 gui_elements_to_hide = [ 6944 self._view.ui.btn_pred_analysis_multi_remove, 6945 self._view.ui.btn_pred_analysis_multi_add, 6946 self._view.ui.box_pred_analysis_multi_prot_struct_1, 6947 self._view.ui.box_pred_analysis_multi_prot_struct_2, 6948 self._view.ui.btn_pred_analysis_multi_back_3, 6949 self._view.ui.btn_pred_analysis_multi_next_2, 6950 self._view.ui.btn_pred_analysis_multi_back_4, 6951 self._view.ui.btn_pred_analysis_multi_next_3, 6952 self._view.ui.lbl_pred_analysis_multi_images, 6953 self._view.ui.cb_pred_analysis_multi_images, 6954 self._view.ui.btn_pred_analysis_multi_start, 6955 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 6956 ] 6957 gui_utils.show_gui_elements(gui_elements_to_show) 6958 gui_utils.hide_gui_elements(gui_elements_to_hide) 6959 self._view.ui.list_pred_analysis_multi_model_chains.clear() 6960 self._view.ui.list_pred_analysis_multi_ref_chains.setEnabled(False) 6961 self._view.ui.btn_pred_analysis_multi_next_4.setEnabled(False) 6962 6963 for i in range(self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount()): 6964 if ( 6965 self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem(i).text() 6966 == self._view.ui.box_pred_analysis_multi_prot_struct_2.currentText() 6967 ): 6968 self._view.ui.list_pred_analysis_multi_model_chains.addItem( 6969 self._view.ui.table_pred_analysis_multi_prot_to_predict.item(i, 0).text(), 6970 ) 6971 if self._view.ui.list_pred_analysis_multi_model_chains.count() == 0: 6972 tmp_protein = self._current_project.search_protein( 6973 self._view.ui.box_pred_analysis_multi_prot_struct_2.currentText(), 6974 ) 6975 for tmp_chain in tmp_protein.chains: 6976 if tmp_chain.chain_type == "protein_chain": 6977 self._view.ui.list_pred_analysis_multi_model_chains.addItem(tmp_chain.chain_letter) 6978 if len(self._view.ui.list_pred_analysis_multi_ref_chains.selectedItems()) == 1: 6979 self._view.ui.lbl_pred_analysis_multi_model_chains.setText( 6980 f"Select 1 chain in protein structure {self._view.ui.lbl_pred_analysis_multi_prot_struct_2.text()}.", 6981 ) 6982 else: 6983 self._view.ui.lbl_pred_analysis_multi_model_chains.setText( 6984 f"Select {len(self._view.ui.list_pred_analysis_multi_ref_chains.selectedItems())} chains in " 6985 f"protein structure {self._view.ui.lbl_pred_analysis_multi_prot_struct_2.text()}.", 6986 ) 6987 6988 def multi_pred_analysis_structure_analysis_back_4(self) -> None: 6989 """Hides the gui elements to select the chains in protein 1.""" 6990 gui_elements_to_show = [ 6991 self._view.ui.lbl_pred_analysis_multi_overview, 6992 self._view.ui.list_pred_analysis_multi_overview, 6993 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 6994 self._view.ui.box_pred_analysis_multi_prot_struct_1, 6995 self._view.ui.lbl_analysis_batch_vs_3, 6996 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 6997 self._view.ui.box_pred_analysis_multi_prot_struct_2, 6998 self._view.ui.btn_pred_analysis_multi_back_3, 6999 self._view.ui.btn_pred_analysis_multi_next_2, 7000 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 7001 ] 7002 gui_elements_to_hide = [ 7003 self._view.ui.btn_pred_analysis_multi_remove, 7004 self._view.ui.btn_pred_analysis_multi_add, 7005 self._view.ui.lbl_pred_analysis_multi_ref_chains, 7006 self._view.ui.list_pred_analysis_multi_ref_chains, 7007 self._view.ui.btn_pred_analysis_multi_back_4, 7008 self._view.ui.btn_pred_analysis_multi_next_3, 7009 self._view.ui.lbl_pred_analysis_multi_model_chains, 7010 self._view.ui.list_pred_analysis_multi_model_chains, 7011 self._view.ui.btn_pred_analysis_multi_back_5, 7012 self._view.ui.btn_pred_analysis_multi_next_4, 7013 self._view.ui.lbl_pred_analysis_multi_images, 7014 self._view.ui.cb_pred_analysis_multi_images, 7015 self._view.ui.btn_pred_analysis_multi_start, 7016 ] 7017 gui_utils.show_gui_elements(gui_elements_to_show) 7018 gui_utils.hide_gui_elements(gui_elements_to_hide) 7019 self._view.ui.lbl_pred_analysis_multi_prot_struct_1.setText("Protein structure 1") 7020 self._view.ui.lbl_pred_analysis_multi_prot_struct_2.setText("Protein structure 2") 7021 7022 def multi_pred_analysis_structure_analysis_next_4(self) -> None: 7023 """Adds the protein pair to the list of protein pairs to analyze.""" 7024 gui_elements_to_show = [ 7025 self._view.ui.btn_pred_analysis_multi_remove, 7026 self._view.ui.btn_pred_analysis_multi_add, 7027 self._view.ui.lbl_pred_analysis_multi_overview, 7028 self._view.ui.list_pred_analysis_multi_overview, 7029 self._view.ui.lbl_pred_analysis_multi_images, 7030 self._view.ui.cb_pred_analysis_multi_images, 7031 self._view.ui.btn_pred_analysis_multi_start, 7032 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 7033 ] 7034 gui_elements_to_hide = [ 7035 self._view.ui.box_pred_analysis_multi_prot_struct_1, 7036 self._view.ui.box_pred_analysis_multi_prot_struct_2, 7037 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 7038 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 7039 self._view.ui.lbl_analysis_batch_vs_3, 7040 self._view.ui.lbl_pred_analysis_multi_ref_chains, 7041 self._view.ui.list_pred_analysis_multi_ref_chains, 7042 self._view.ui.lbl_pred_analysis_multi_model_chains, 7043 self._view.ui.list_pred_analysis_multi_model_chains, 7044 self._view.ui.btn_pred_analysis_multi_back_3, 7045 self._view.ui.btn_pred_analysis_multi_next_2, 7046 self._view.ui.btn_pred_analysis_multi_back_4, 7047 self._view.ui.btn_pred_analysis_multi_next_3, 7048 self._view.ui.btn_pred_analysis_multi_back_5, 7049 self._view.ui.btn_pred_analysis_multi_next_4, 7050 ] 7051 gui_utils.show_gui_elements(gui_elements_to_show) 7052 gui_utils.hide_gui_elements(gui_elements_to_hide) 7053 prot_1_name = self._view.ui.lbl_pred_analysis_multi_prot_struct_1.text() 7054 prot_1_chains = [] 7055 for chain in self._view.ui.list_pred_analysis_multi_ref_chains.selectedItems(): 7056 prot_1_chains.append(chain.text()) 7057 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 7058 prot_2_name = self._view.ui.lbl_pred_analysis_multi_prot_struct_2.text() 7059 prot_2_chains = [] 7060 for chain in self._view.ui.list_pred_analysis_multi_model_chains.selectedItems(): 7061 prot_2_chains.append(chain.text()) 7062 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 7063 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 7064 item = QtWidgets.QListWidgetItem(analysis_name) 7065 self._view.ui.list_pred_analysis_multi_overview.addItem(item) 7066 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(False) 7067 7068 def multi_pred_analysis_structure_analysis_back_5(self) -> None: 7069 """Hides the gui elements to select the chains in protein 2.""" 7070 gui_elements_to_show = [ 7071 self._view.ui.lbl_pred_analysis_multi_overview, 7072 self._view.ui.list_pred_analysis_multi_overview, 7073 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 7074 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 7075 self._view.ui.lbl_analysis_batch_vs_3, 7076 self._view.ui.lbl_pred_analysis_multi_ref_chains, 7077 self._view.ui.list_pred_analysis_multi_ref_chains, 7078 self._view.ui.btn_pred_analysis_multi_back_4, 7079 self._view.ui.btn_pred_analysis_multi_next_3, 7080 ] 7081 gui_elements_to_hide = [ 7082 self._view.ui.btn_pred_analysis_multi_remove, 7083 self._view.ui.btn_pred_analysis_multi_add, 7084 self._view.ui.box_pred_analysis_multi_prot_struct_1, 7085 self._view.ui.box_pred_analysis_multi_prot_struct_2, 7086 self._view.ui.btn_pred_analysis_multi_back_3, 7087 self._view.ui.btn_pred_analysis_multi_next_2, 7088 self._view.ui.btn_pred_analysis_multi_back_5, 7089 self._view.ui.btn_pred_analysis_multi_next_4, 7090 self._view.ui.lbl_pred_analysis_multi_images, 7091 self._view.ui.cb_pred_analysis_multi_images, 7092 self._view.ui.btn_pred_analysis_multi_start, 7093 self._view.ui.lbl_pred_analysis_multi_model_chains, 7094 self._view.ui.list_pred_analysis_multi_model_chains, 7095 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 7096 ] 7097 gui_utils.show_gui_elements(gui_elements_to_show) 7098 gui_utils.hide_gui_elements(gui_elements_to_hide) 7099 self._view.ui.list_pred_analysis_multi_ref_chains.setEnabled(True) 7100 7101 # tmp_protein = self._current_project.search_protein(self._view.ui.box_pred_analysis_multi_prot_struct_2.currentText()) 7102 # for tmp_chain in tmp_protein.chains: 7103 # if tmp_chain.chain_type == "protein_chain": 7104 # self._view.ui.list_pred_analysis_multi_ref_chains.addItem(tmp_chain.chain_letter) 7105 7106 def multi_pred_analysis_structure_analysis_overview_clicked(self) -> None: 7107 """Enables the remove button.""" 7108 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(True) 7109 7110 def fill_multi_pred_analysis_protein_boxes(self) -> None: 7111 """Fills the combo boxes with the protein names.""" 7112 protein_names = [] 7113 for i in range(self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount()): 7114 protein_names.append(self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem(i).text()) 7115 for tmp_protein in self._current_project.proteins: 7116 protein_names.append(tmp_protein.get_molecule_object()) 7117 protein_names.insert(0, "") 7118 protein_names = list(set(protein_names)) 7119 self._view.ui.box_pred_analysis_multi_prot_struct_1.clear() 7120 self._view.ui.box_pred_analysis_multi_prot_struct_2.clear() 7121 gui_utils.fill_combo_box(self._view.ui.box_pred_analysis_multi_prot_struct_1, protein_names) 7122 gui_utils.fill_combo_box(self._view.ui.box_pred_analysis_multi_prot_struct_2, protein_names) 7123 7124 def remove_multi_pred_analysis_analysis_run(self) -> None: 7125 """Removes the selected protein pair from the list of protein pairs to analyze.""" 7126 self._view.ui.list_pred_analysis_multi_overview.takeItem( 7127 self._view.ui.list_pred_analysis_multi_overview.currentRow(), 7128 ) 7129 gui_elements_to_show = [ 7130 self._view.ui.lbl_pred_analysis_multi_overview, 7131 self._view.ui.list_pred_analysis_multi_overview, 7132 self._view.ui.btn_pred_analysis_multi_add, 7133 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 7134 ] 7135 gui_elements_to_hide = [ 7136 self._view.ui.btn_pred_analysis_multi_remove, 7137 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 7138 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 7139 self._view.ui.lbl_analysis_batch_vs_3, 7140 self._view.ui.lbl_pred_analysis_multi_ref_chains, 7141 self._view.ui.list_pred_analysis_multi_ref_chains, 7142 self._view.ui.btn_pred_analysis_multi_back_4, 7143 self._view.ui.btn_pred_analysis_multi_next_3, 7144 self._view.ui.box_pred_analysis_multi_prot_struct_1, 7145 self._view.ui.box_pred_analysis_multi_prot_struct_2, 7146 self._view.ui.btn_pred_analysis_multi_back_3, 7147 self._view.ui.btn_pred_analysis_multi_next_2, 7148 self._view.ui.lbl_pred_analysis_multi_model_chains, 7149 self._view.ui.list_pred_analysis_multi_model_chains, 7150 self._view.ui.btn_pred_analysis_multi_back_5, 7151 self._view.ui.btn_pred_analysis_multi_next_4, 7152 self._view.ui.lbl_pred_analysis_multi_images, 7153 self._view.ui.cb_pred_analysis_multi_images, 7154 self._view.ui.btn_pred_analysis_multi_start, 7155 ] 7156 gui_utils.show_gui_elements(gui_elements_to_show) 7157 gui_utils.hide_gui_elements(gui_elements_to_hide) 7158 if self._view.ui.list_pred_analysis_multi_overview.count() > 0: 7159 self._view.ui.btn_pred_analysis_multi_remove.show() 7160 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(False) 7161 self._view.ui.btn_pred_analysis_multi_start.show() 7162 self._view.ui.lbl_pred_analysis_multi_images.show() 7163 self._view.ui.cb_pred_analysis_multi_images.show() 7164 # if self._view.ui.list_pred_analysis_multi_overview.count() == 0: 7165 # 7166 # self._view.ui.btn_pred_analysis_multi_back_pred_setup.show() 7167 # self._view.ui.btn_pred_analysis_multi_remove.hide() 7168 7169 def check_multi_pred_analysis_if_same_no_of_chains_selected(self) -> None: 7170 """Checks if the same number of chains were selected.""" 7171 self._view.ui.btn_pred_analysis_multi_next_4.setEnabled(False) 7172 if self.no_of_selected_chains == len(self._view.ui.list_pred_analysis_multi_model_chains.selectedItems()): 7173 self._view.ui.btn_pred_analysis_multi_next_4.setEnabled(True) 7174 7175 prot_1_name = self._view.ui.lbl_pred_analysis_multi_prot_struct_1.text() 7176 prot_1_chains = [] 7177 for chain in self._view.ui.list_pred_analysis_multi_ref_chains.selectedItems(): 7178 prot_1_chains.append(chain.text()) 7179 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 7180 prot_2_name = self._view.ui.lbl_pred_analysis_multi_prot_struct_2.text() 7181 prot_2_chains = [] 7182 for chain in self._view.ui.list_pred_analysis_multi_model_chains.selectedItems(): 7183 prot_2_chains.append(chain.text()) 7184 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 7185 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 7186 for tmp_row in range(self._view.ui.list_pred_analysis_multi_overview.count()): 7187 if analysis_name == self._view.ui.list_pred_analysis_multi_overview.item(tmp_row).text(): 7188 self._view.ui.btn_pred_analysis_multi_next_4.setEnabled(False) 7189 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_multi_next_4) 7190 return 7191 7192 def check_multi_pred_analysis_if_prot_structs_are_filled(self) -> None: 7193 """Checks if two proteins were selected.""" 7194 prot_1 = self._view.ui.box_pred_analysis_multi_prot_struct_1.itemText( 7195 self._view.ui.box_pred_analysis_multi_prot_struct_1.currentIndex(), 7196 ) 7197 prot_2 = self._view.ui.box_pred_analysis_multi_prot_struct_2.itemText( 7198 self._view.ui.box_pred_analysis_multi_prot_struct_2.currentIndex(), 7199 ) 7200 if prot_1 != "" and prot_2 != "": 7201 self._view.ui.btn_pred_analysis_multi_next_2.setEnabled(True) 7202 else: 7203 self._view.ui.btn_pred_analysis_multi_next_2.setEnabled(False) 7204 7205 def count_multi_pred_analysis_selected_chains_for_prot_struct_1(self) -> None: 7206 """Counts the number of chains in protein 1.""" 7207 self.no_of_selected_chains = len(self._view.ui.list_pred_analysis_multi_ref_chains.selectedItems()) 7208 if self.no_of_selected_chains > 0: 7209 self._view.ui.btn_pred_analysis_multi_next_3.setEnabled(True) 7210 else: 7211 self._view.ui.btn_pred_analysis_multi_next_3.setEnabled(False) 7212 7213 # </editor-fold> 7214 # </editor-fold> 7215 7216 # <editor-fold desc="Distance analysis"> 7217 def structure_analysis_add(self) -> None: 7218 """Shows the gui elements to choose the two proteins.""" 7219 gui_elements_to_show = [ 7220 self._view.ui.lbl_analysis_batch_overview, 7221 self._view.ui.list_analysis_batch_overview, 7222 self._view.ui.lbl_analysis_batch_prot_struct_1, 7223 self._view.ui.box_analysis_batch_prot_struct_1, 7224 self._view.ui.lbl_analysis_batch_vs, 7225 self._view.ui.lbl_analysis_batch_prot_struct_2, 7226 self._view.ui.box_analysis_batch_prot_struct_2, 7227 self._view.ui.btn_analysis_batch_back, 7228 self._view.ui.btn_analysis_batch_next, 7229 ] 7230 gui_elements_to_hide = [ 7231 self._view.ui.btn_analysis_batch_remove, 7232 self._view.ui.btn_analysis_batch_add, 7233 self._view.ui.lbl_analysis_batch_ref_chains, 7234 self._view.ui.list_analysis_batch_ref_chains, 7235 self._view.ui.btn_analysis_batch_back_2, 7236 self._view.ui.btn_analysis_batch_next_2, 7237 self._view.ui.lbl_analysis_batch_model_chains, 7238 self._view.ui.list_analysis_batch_model_chains, 7239 self._view.ui.btn_analysis_batch_back_3, 7240 self._view.ui.btn_analysis_batch_next_3, 7241 self._view.ui.lbl_analysis_batch_images, 7242 self._view.ui.cb_analysis_batch_images, 7243 self._view.ui.btn_analysis_batch_start, 7244 ] 7245 7246 gui_utils.show_gui_elements(gui_elements_to_show) 7247 gui_utils.hide_gui_elements(gui_elements_to_hide) 7248 self._view.ui.lbl_analysis_batch_prot_struct_1.clear() 7249 self._view.ui.lbl_analysis_batch_prot_struct_2.clear() 7250 self._view.ui.lbl_analysis_batch_prot_struct_1.setText("Protein structure 1") 7251 self._view.ui.lbl_analysis_batch_prot_struct_2.setText("Protein structure 2") 7252 self.fill_protein_boxes_batch() 7253 if self._view.ui.list_analysis_batch_overview.count() > 0: 7254 try: 7255 self._view.ui.list_analysis_batch_overview.currentItem().setSelected(False) 7256 except AttributeError: 7257 constants.PYSSA_LOGGER.debug("No selection in struction analysis overview.") 7258 7259 def structure_analysis_back(self) -> None: 7260 """Hides the gui elements to choose the two proteins.""" 7261 gui_elements_to_show = [ 7262 self._view.ui.lbl_analysis_batch_overview, 7263 self._view.ui.list_analysis_batch_overview, 7264 self._view.ui.btn_analysis_batch_add, 7265 ] 7266 gui_elements_to_hide = [ 7267 self._view.ui.btn_analysis_batch_remove, 7268 self._view.ui.lbl_analysis_batch_prot_struct_1, 7269 self._view.ui.lbl_analysis_batch_prot_struct_2, 7270 self._view.ui.lbl_analysis_batch_vs, 7271 self._view.ui.lbl_analysis_batch_ref_chains, 7272 self._view.ui.list_analysis_batch_ref_chains, 7273 self._view.ui.btn_analysis_batch_back_2, 7274 self._view.ui.btn_analysis_batch_next_2, 7275 self._view.ui.box_analysis_batch_prot_struct_1, 7276 self._view.ui.box_analysis_batch_prot_struct_2, 7277 self._view.ui.btn_analysis_batch_back, 7278 self._view.ui.btn_analysis_batch_next, 7279 self._view.ui.lbl_analysis_batch_model_chains, 7280 self._view.ui.list_analysis_batch_model_chains, 7281 self._view.ui.btn_analysis_batch_back_3, 7282 self._view.ui.btn_analysis_batch_next_3, 7283 self._view.ui.lbl_analysis_batch_images, 7284 self._view.ui.cb_analysis_batch_images, 7285 self._view.ui.btn_analysis_batch_start, 7286 ] 7287 gui_utils.show_gui_elements(gui_elements_to_show) 7288 gui_utils.hide_gui_elements(gui_elements_to_hide) 7289 if self._view.ui.list_analysis_batch_overview.count() > 0: 7290 self._view.ui.btn_analysis_batch_remove.show() 7291 self._view.ui.btn_analysis_batch_remove.setEnabled(False) 7292 self._view.ui.btn_analysis_batch_start.show() 7293 self._view.ui.lbl_analysis_batch_images.show() 7294 self._view.ui.cb_analysis_batch_images.show() 7295 7296 def structure_analysis_next_2(self) -> None: 7297 """Shows the gui elements to select the chains in protein 2.""" 7298 gui_elements_to_show = [ 7299 self._view.ui.lbl_analysis_batch_overview, 7300 self._view.ui.list_analysis_batch_overview, 7301 self._view.ui.lbl_analysis_batch_prot_struct_1, 7302 self._view.ui.lbl_analysis_batch_prot_struct_2, 7303 self._view.ui.lbl_analysis_batch_vs, 7304 self._view.ui.lbl_analysis_batch_ref_chains, 7305 self._view.ui.list_analysis_batch_ref_chains, 7306 self._view.ui.lbl_analysis_batch_model_chains, 7307 self._view.ui.list_analysis_batch_model_chains, 7308 self._view.ui.btn_analysis_batch_back_3, 7309 self._view.ui.btn_analysis_batch_next_3, 7310 ] 7311 gui_elements_to_hide = [ 7312 self._view.ui.btn_analysis_batch_remove, 7313 self._view.ui.btn_analysis_batch_add, 7314 self._view.ui.box_analysis_batch_prot_struct_1, 7315 self._view.ui.box_analysis_batch_prot_struct_2, 7316 self._view.ui.btn_analysis_batch_back, 7317 self._view.ui.btn_analysis_batch_next, 7318 self._view.ui.btn_analysis_batch_back_2, 7319 self._view.ui.btn_analysis_batch_next_2, 7320 self._view.ui.lbl_analysis_batch_images, 7321 self._view.ui.cb_analysis_batch_images, 7322 self._view.ui.btn_analysis_batch_start, 7323 ] 7324 gui_utils.show_gui_elements(gui_elements_to_show) 7325 gui_utils.hide_gui_elements(gui_elements_to_hide) 7326 self._view.ui.list_analysis_batch_model_chains.clear() 7327 self._view.ui.list_analysis_batch_ref_chains.setEnabled(False) 7328 self._view.ui.btn_analysis_batch_next_3.setEnabled(False) 7329 7330 tmp_protein = self._current_project.search_protein(self._view.ui.box_analysis_batch_prot_struct_2.currentText()) 7331 for tmp_chain in tmp_protein.chains: 7332 if tmp_chain.chain_type == "protein_chain": 7333 self._view.ui.list_analysis_batch_model_chains.addItem(tmp_chain.chain_letter) 7334 if len(self._view.ui.list_analysis_batch_ref_chains.selectedItems()) == 1: 7335 self._view.ui.lbl_analysis_batch_model_chains.setText( 7336 f"Select 1 chain in protein structure {self._view.ui.lbl_analysis_batch_prot_struct_2.text()}.", 7337 ) 7338 else: 7339 self._view.ui.lbl_analysis_batch_model_chains.setText( 7340 f"Select {len(self._view.ui.list_analysis_batch_ref_chains.selectedItems())} chains in " 7341 f"protein structure {self._view.ui.lbl_analysis_batch_prot_struct_2.text()}.", 7342 ) 7343 7344 def structure_analysis_back_2(self) -> None: 7345 """Hides the gui elements to select the chains in protein 1.""" 7346 gui_elements_to_show = [ 7347 self._view.ui.lbl_analysis_batch_overview, 7348 self._view.ui.list_analysis_batch_overview, 7349 self._view.ui.lbl_analysis_batch_prot_struct_1, 7350 self._view.ui.box_analysis_batch_prot_struct_1, 7351 self._view.ui.lbl_analysis_batch_vs, 7352 self._view.ui.lbl_analysis_batch_prot_struct_2, 7353 self._view.ui.box_analysis_batch_prot_struct_2, 7354 self._view.ui.btn_analysis_batch_back, 7355 self._view.ui.btn_analysis_batch_next, 7356 ] 7357 gui_elements_to_hide = [ 7358 self._view.ui.btn_analysis_batch_remove, 7359 self._view.ui.btn_analysis_batch_add, 7360 self._view.ui.lbl_analysis_batch_ref_chains, 7361 self._view.ui.list_analysis_batch_ref_chains, 7362 self._view.ui.btn_analysis_batch_back_2, 7363 self._view.ui.btn_analysis_batch_next_2, 7364 self._view.ui.lbl_analysis_batch_model_chains, 7365 self._view.ui.list_analysis_batch_model_chains, 7366 self._view.ui.btn_analysis_batch_back_3, 7367 self._view.ui.btn_analysis_batch_next_3, 7368 self._view.ui.lbl_analysis_batch_images, 7369 self._view.ui.cb_analysis_batch_images, 7370 self._view.ui.btn_analysis_batch_start, 7371 ] 7372 gui_utils.show_gui_elements(gui_elements_to_show) 7373 gui_utils.hide_gui_elements(gui_elements_to_hide) 7374 self._view.ui.lbl_analysis_batch_prot_struct_1.setText("Protein structure 1") 7375 self._view.ui.lbl_analysis_batch_prot_struct_2.setText("Protein structure 2") 7376 7377 def structure_analysis_next_3(self) -> None: 7378 """Adds the protein pair to the list of protein pairs to analyze.""" 7379 gui_elements_to_show = [ 7380 self._view.ui.btn_analysis_batch_remove, 7381 self._view.ui.btn_analysis_batch_add, 7382 self._view.ui.lbl_analysis_batch_overview, 7383 self._view.ui.list_analysis_batch_overview, 7384 self._view.ui.lbl_analysis_batch_images, 7385 self._view.ui.cb_analysis_batch_images, 7386 self._view.ui.btn_analysis_batch_start, 7387 ] 7388 gui_elements_to_hide = [ 7389 self._view.ui.box_analysis_batch_prot_struct_1, 7390 self._view.ui.box_analysis_batch_prot_struct_2, 7391 self._view.ui.lbl_analysis_batch_prot_struct_1, 7392 self._view.ui.lbl_analysis_batch_prot_struct_2, 7393 self._view.ui.lbl_analysis_batch_vs, 7394 self._view.ui.lbl_analysis_batch_ref_chains, 7395 self._view.ui.list_analysis_batch_ref_chains, 7396 self._view.ui.lbl_analysis_batch_model_chains, 7397 self._view.ui.list_analysis_batch_model_chains, 7398 self._view.ui.btn_analysis_batch_back, 7399 self._view.ui.btn_analysis_batch_next, 7400 self._view.ui.btn_analysis_batch_back_2, 7401 self._view.ui.btn_analysis_batch_next_2, 7402 self._view.ui.btn_analysis_batch_back_3, 7403 self._view.ui.btn_analysis_batch_next_3, 7404 ] 7405 gui_utils.show_gui_elements(gui_elements_to_show) 7406 gui_utils.hide_gui_elements(gui_elements_to_hide) 7407 prot_1_name = self._view.ui.lbl_analysis_batch_prot_struct_1.text() 7408 prot_1_chains = [] 7409 for chain in self._view.ui.list_analysis_batch_ref_chains.selectedItems(): 7410 prot_1_chains.append(chain.text()) 7411 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 7412 prot_2_name = self._view.ui.lbl_analysis_batch_prot_struct_2.text() 7413 prot_2_chains = [] 7414 for chain in self._view.ui.list_analysis_batch_model_chains.selectedItems(): 7415 prot_2_chains.append(chain.text()) 7416 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 7417 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 7418 item = QtWidgets.QListWidgetItem(analysis_name) 7419 self._view.ui.list_analysis_batch_overview.addItem(item) 7420 self._view.ui.btn_analysis_batch_remove.setEnabled(False) 7421 7422 def structure_analysis_back_3(self) -> None: 7423 """Hides the gui elements to select the chains in protein 2.""" 7424 gui_elements_to_show = [ 7425 self._view.ui.lbl_analysis_batch_overview, 7426 self._view.ui.list_analysis_batch_overview, 7427 self._view.ui.lbl_analysis_batch_prot_struct_1, 7428 self._view.ui.lbl_analysis_batch_prot_struct_2, 7429 self._view.ui.lbl_analysis_batch_vs, 7430 self._view.ui.lbl_analysis_batch_ref_chains, 7431 self._view.ui.list_analysis_batch_ref_chains, 7432 self._view.ui.btn_analysis_batch_back_2, 7433 self._view.ui.btn_analysis_batch_next_2, 7434 ] 7435 gui_elements_to_hide = [ 7436 self._view.ui.btn_analysis_batch_remove, 7437 self._view.ui.btn_analysis_batch_add, 7438 self._view.ui.box_analysis_batch_prot_struct_1, 7439 self._view.ui.box_analysis_batch_prot_struct_2, 7440 self._view.ui.btn_analysis_batch_back, 7441 self._view.ui.btn_analysis_batch_next, 7442 self._view.ui.btn_analysis_batch_back_3, 7443 self._view.ui.btn_analysis_batch_next_3, 7444 self._view.ui.lbl_analysis_batch_images, 7445 self._view.ui.cb_analysis_batch_images, 7446 self._view.ui.btn_analysis_batch_start, 7447 self._view.ui.lbl_analysis_batch_model_chains, 7448 self._view.ui.list_analysis_batch_model_chains, 7449 ] 7450 gui_utils.show_gui_elements(gui_elements_to_show) 7451 gui_utils.hide_gui_elements(gui_elements_to_hide) 7452 self._view.ui.list_analysis_batch_ref_chains.setEnabled(True) 7453 7454 # tmp_protein = self._current_project.search_protein(self._view.ui.box_analysis_batch_prot_struct_2.currentText()) 7455 # for tmp_chain in tmp_protein.chains: 7456 # if tmp_chain.chain_type == "protein_chain": 7457 # self._view.ui.list_analysis_batch_ref_chains.addItem(tmp_chain.chain_letter) 7458 7459 def structure_analysis_overview_clicked(self) -> None: 7460 """Enables the remove button.""" 7461 self._view.ui.btn_analysis_batch_remove.setEnabled(True) 7462 7463 def fill_protein_boxes_batch(self) -> None: 7464 """Fills the combo boxes with the protein names.""" 7465 proteins = [] 7466 for tmp_protein in self._current_project.proteins: 7467 proteins.append(tmp_protein.get_molecule_object()) 7468 proteins.insert(0, "") 7469 self._view.ui.box_analysis_batch_prot_struct_1.clear() 7470 self._view.ui.box_analysis_batch_prot_struct_2.clear() 7471 gui_utils.fill_combo_box(self._view.ui.box_analysis_batch_prot_struct_1, proteins) 7472 gui_utils.fill_combo_box(self._view.ui.box_analysis_batch_prot_struct_2, proteins) 7473 7474 def remove_analysis_run(self) -> None: 7475 """Removes the selected protein pair from the list of protein pairs to analyze.""" 7476 self._view.ui.list_analysis_batch_overview.takeItem(self._view.ui.list_analysis_batch_overview.currentRow()) 7477 if self._view.ui.list_analysis_batch_overview.count() == 0: 7478 gui_elements_to_show = [ 7479 self._view.ui.lbl_analysis_batch_overview, 7480 self._view.ui.list_analysis_batch_overview, 7481 self._view.ui.btn_analysis_batch_add, 7482 ] 7483 7484 gui_elements_to_hide = [ 7485 self._view.ui.btn_analysis_batch_remove, 7486 self._view.ui.lbl_analysis_batch_prot_struct_1, 7487 self._view.ui.lbl_analysis_batch_prot_struct_2, 7488 self._view.ui.lbl_analysis_batch_vs, 7489 self._view.ui.lbl_analysis_batch_ref_chains, 7490 self._view.ui.list_analysis_batch_ref_chains, 7491 self._view.ui.btn_analysis_batch_back_2, 7492 self._view.ui.btn_analysis_batch_next_2, 7493 self._view.ui.box_analysis_batch_prot_struct_1, 7494 self._view.ui.box_analysis_batch_prot_struct_2, 7495 self._view.ui.btn_analysis_batch_back, 7496 self._view.ui.btn_analysis_batch_next, 7497 self._view.ui.lbl_analysis_batch_model_chains, 7498 self._view.ui.list_analysis_batch_model_chains, 7499 self._view.ui.btn_analysis_batch_back_3, 7500 self._view.ui.btn_analysis_batch_next_3, 7501 self._view.ui.lbl_analysis_batch_images, 7502 self._view.ui.cb_analysis_batch_images, 7503 self._view.ui.btn_analysis_batch_start, 7504 ] 7505 7506 gui_utils.show_gui_elements(gui_elements_to_show) 7507 gui_utils.hide_gui_elements(gui_elements_to_hide) 7508 self._view.ui.btn_analysis_batch_remove.hide() 7509 else: 7510 if self._view.ui.list_analysis_batch_overview.count() > 0: 7511 try: 7512 self._view.ui.list_analysis_batch_overview.currentItem().setSelected(False) 7513 except AttributeError: 7514 constants.PYSSA_LOGGER.debug("No selection in struction analysis overview.") 7515 self._view.ui.btn_analysis_batch_remove.setEnabled(False) 7516 7517 def check_if_same_no_of_chains_selected_batch(self) -> None: 7518 """Checks if the same number of proteins were selected.""" 7519 self._view.ui.btn_analysis_batch_next_3.setEnabled(False) 7520 if self.no_of_selected_chains == len(self._view.ui.list_analysis_batch_model_chains.selectedItems()): 7521 self._view.ui.btn_analysis_batch_next_3.setEnabled(True) 7522 7523 prot_1_name = self._view.ui.lbl_analysis_batch_prot_struct_1.text() 7524 prot_1_chains = [] 7525 for chain in self._view.ui.list_analysis_batch_ref_chains.selectedItems(): 7526 prot_1_chains.append(chain.text()) 7527 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 7528 prot_2_name = self._view.ui.lbl_analysis_batch_prot_struct_2.text() 7529 prot_2_chains = [] 7530 for chain in self._view.ui.list_analysis_batch_model_chains.selectedItems(): 7531 prot_2_chains.append(chain.text()) 7532 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 7533 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 7534 for tmp_row in range(self._view.ui.list_analysis_batch_overview.count()): 7535 if analysis_name == self._view.ui.list_analysis_batch_overview.item(tmp_row).text(): 7536 self._view.ui.btn_analysis_batch_next_3.setEnabled(False) 7537 styles.color_button_not_ready(self._view.ui.btn_analysis_batch_next_3) 7538 return 7539 7540 def check_if_prot_structs_are_filled_batch(self) -> None: 7541 """Checks if two proteins were selected.""" 7542 prot_1 = self._view.ui.box_analysis_batch_prot_struct_1.itemText( 7543 self._view.ui.box_analysis_batch_prot_struct_1.currentIndex(), 7544 ) 7545 prot_2 = self._view.ui.box_analysis_batch_prot_struct_2.itemText( 7546 self._view.ui.box_analysis_batch_prot_struct_2.currentIndex(), 7547 ) 7548 if prot_1 != "" and prot_2 != "": 7549 self._view.ui.btn_analysis_batch_next.setEnabled(True) 7550 else: 7551 self._view.ui.btn_analysis_batch_next.setEnabled(False) 7552 7553 def count_batch_selected_chains_for_prot_struct_1(self) -> None: 7554 """Counts the number of chains of protein 1.""" 7555 self.no_of_selected_chains = len(self._view.ui.list_analysis_batch_ref_chains.selectedItems()) 7556 if self.no_of_selected_chains > 0: 7557 self._view.ui.btn_analysis_batch_next_2.setEnabled(True) 7558 else: 7559 self._view.ui.btn_analysis_batch_next_2.setEnabled(False) 7560 7561 # </editor-fold> 7562 7563 # <editor-fold desc="Analysis images"> 7564 def display_image_analysis_page(self) -> None: 7565 """Displays the analysis image work area.""" 7566 # get all protein pairs without images 7567 self._view.ui.list_analysis_images_struct_analysis.clear() 7568 self._view.ui.list_analysis_images_creation_struct_analysis.clear() 7569 for tmp_protein_pair in self._current_project.protein_pairs: 7570 if len(tmp_protein_pair.distance_analysis.analysis_results.structure_aln_image) == 0: 7571 self._view.ui.list_analysis_images_struct_analysis.addItem(tmp_protein_pair.name) 7572 self.last_sidebar_button = styles.color_sidebar_buttons( 7573 self.last_sidebar_button, 7574 self._view.ui.btn_image_analysis_page, 7575 ) 7576 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 23, "Analysis Images") 7577 self._view.ui.btn_add_analysis_images_struct_analysis.setEnabled(False) 7578 self._view.ui.btn_remove_analysis_images_creation_struct_analysis.setEnabled(False) 7579 self._view.ui.btn_start_automatic_image_creation.setEnabled(False) 7580 7581 def analysis_images_enable_add(self) -> None: 7582 """Enables the add button.""" 7583 self._view.ui.btn_add_analysis_images_struct_analysis.setEnabled(True) 7584 7585 def analysis_images_enable_remove(self) -> None: 7586 """Enables the remove button.""" 7587 self._view.ui.btn_remove_analysis_images_creation_struct_analysis.setEnabled(True) 7588 7589 def add_protein_pair_to_image_creation_queue(self) -> None: 7590 """Adds a protein pair from the list of protein pairs to make images of.""" 7591 protein_pair_to_add = self._view.ui.list_analysis_images_struct_analysis.currentItem().text() 7592 self._view.ui.list_analysis_images_creation_struct_analysis.addItem(protein_pair_to_add) 7593 self._view.ui.list_analysis_images_struct_analysis.takeItem( 7594 self._view.ui.list_analysis_images_struct_analysis.currentRow(), 7595 ) 7596 self._view.ui.btn_add_analysis_images_struct_analysis.setEnabled(False) 7597 self.analysis_images_check_if_creation_can_start() 7598 7599 def remove_protein_pair_from_image_creation_queue(self) -> None: 7600 """Removes a protein pair from the list of protein pairs to make images of.""" 7601 protein_pair_to_remove = self._view.ui.list_analysis_images_creation_struct_analysis.currentItem() 7602 self._view.ui.list_analysis_images_creation_struct_analysis.takeItem( 7603 self._view.ui.list_analysis_images_creation_struct_analysis.currentRow(), 7604 ) 7605 self._view.ui.list_analysis_images_struct_analysis.addItem(protein_pair_to_remove) 7606 self._view.ui.btn_remove_analysis_images_creation_struct_analysis.setEnabled(False) 7607 self.analysis_images_check_if_creation_can_start() 7608 7609 def analysis_images_check_if_creation_can_start(self) -> None: 7610 """Checks if the list of protein pairs which get images are empty.""" 7611 if self._view.ui.list_analysis_images_creation_struct_analysis.count() > 0: 7612 self._view.ui.btn_start_automatic_image_creation.setEnabled(True) 7613 else: 7614 self._view.ui.btn_start_automatic_image_creation.setEnabled(False) 7615 7616 # </editor-fold> 7617 7618 # </editor-fold> 7619 7620 def update_status(self, message: str) -> None: 7621 """Updates the status bar of the main view with a custom message.""" 7622 self._view.status_bar.showMessage(message)
Class for main presenter of the pyssa plugin.
MainPresenter(a_view: pyssa.gui.ui.views.main_view.MainView)
123 def __init__(self, a_view: "main_view.MainView") -> None: 124 """Constructor. 125 126 Args: 127 a_view: the main view of the pyssa plugin. 128 129 Raises: 130 IllegalArgumentException: If an argument is illegal. 131 """ 132 # <editor-fold desc="Checks"> 133 safeguard.Safeguard.check_if_value_is_not_none(a_view, logger) 134 135 # </editor-fold> 136 137 # <editor-fold desc="Initialize class attributes"> 138 self._view = a_view 139 self._workspace_path = constants.DEFAULT_WORKSPACE_PATH 140 # TODO: settings and project objects get not initialized properly 141 self._application_settings = settings.Settings("", "") 142 self._current_project: "project.Project" = project.Project() 143 self._project_watcher: "project_watcher.ProjectWatcher" = project_watcher.ProjectWatcher(self._current_project) 144 145 # </editor-fold> 146 147 # Check OS 148 main_window_util.check_operating_system() 149 # Create log dir 150 # <editor-fold desc="Program directory check"> 151 filesystem_helpers.create_directory(pathlib.Path(f"{os.path.expanduser('~')}/.pyssa")) 152 filesystem_helpers.create_directory(pathlib.Path(f"{os.path.expanduser('~')}/.pyssa/logs")) 153 constants.PYSSA_LOGGER.info("Checked program and logs directory.") 154 155 # </editor-fold> 156 # Configure settings 157 # <editor-fold desc="Setup App Settings"> 158 self._application_settings = settings.Settings(constants.SETTINGS_DIR, constants.SETTINGS_FILENAME) 159 if not os.path.exists(constants.SETTINGS_FULL_FILEPATH): 160 constants.PYSSA_LOGGER.info("Settings file not found, open configuration dialog.") 161 # Configuration dialog to setup setting file 162 dialog = dialog_startup.DialogStartup() 163 dialog.exec_() 164 165 # checks if the cancel button was pressed 166 if dialog_startup.global_var_terminate_app == 1: 167 os.remove(constants.SETTINGS_FULL_FILEPATH) 168 constants.PYSSA_LOGGER.info("Configuration dialog closed, and removed new settings file.") 169 sys.exit() 170 171 self._application_settings.app_launch = 1 172 self._application_settings.workspace_path = pathlib.Path(dialog_startup.global_var_startup_workspace) 173 174 constants.PYSSA_LOGGER.info("Demo projects are getting downloaded and extracted ...") 175 import zipfile 176 177 with zipfile.ZipFile(pathlib.Path(f"{constants.SETTINGS_DIR}/demo-projects.zip"), "r") as zip_ref: 178 zip_ref.extractall(pathlib.Path(f"{constants.SETTINGS_DIR}/demo-projects")) 179 constants.PYSSA_LOGGER.info( 180 "Demo projects are downloaded and extracted.\n Import of demo projects started ...", 181 ) 182 183 path_of_demo_projects = pathlib.Path(f"{constants.SETTINGS_DIR}/demo-projects") 184 tmp_project = project.Project("", dialog_startup.global_var_startup_workspace) 185 for tmp_filename in os.listdir(path_of_demo_projects): 186 try: 187 tmp_project = tmp_project.deserialize_project( 188 pathlib.Path(f"{path_of_demo_projects}/{tmp_filename}"), 189 self._application_settings, 190 ) 191 except exception.IllegalArgumentError: 192 constants.PYSSA_LOGGER.warning( 193 "The workspace path does not exist on this system, " "but this is due to the demo projects.", 194 ) 195 tmp_project.set_workspace_path(dialog_startup.global_var_startup_workspace) 196 new_filepath = pathlib.Path(f"{dialog_startup.global_var_startup_workspace}/{tmp_filename}") 197 tmp_project.serialize_project(new_filepath) 198 constants.PYSSA_LOGGER.info("Import process of demo projects finished.") 199 try: 200 os.remove(pathlib.Path(f"{constants.SETTINGS_DIR}/demo-projects.zip")) 201 except FileNotFoundError: 202 constants.PYSSA_LOGGER.warning("Zip archive of demo projects could not be found!") 203 constants.PYSSA_LOGGER.info("Serialize settings ...") 204 self._application_settings.serialize_settings() 205 constants.PYSSA_LOGGER.info("Serialize settings finished.") 206 207 QtWidgets.QApplication.restoreOverrideCursor() 208 209 globals.g_settings = main_window_util.setup_app_settings(self._application_settings) 210 self._application_settings = globals.g_settings 211 # </editor-fold> 212 # Check version number 213 main_window_util.check_version_number() 214 215 # <editor-fold desc="Class attributes"> 216 self._workspace_path = self._application_settings.workspace_path 217 self._workspace_status = f"Current workspace: {str(self._workspace_path)}" 218 self._workspace_label = QtWidgets.QLabel(f"Current Workspace: {self._workspace_path}") 219 self.prediction_configuration = prediction_configuration.PredictionConfiguration(True, "pdb70") 220 self.results_name = "" 221 self.no_of_selected_chains = 0 222 self.plot_dialog = QtWidgets.QDialog(self._view) 223 self.view_box = None 224 self.block_box_expert_install = basic_boxes.no_buttons( 225 "Local Colabfold installation", 226 "An installation process is currently running.", 227 QtWidgets.QMessageBox.Information, 228 ) 229 self.prediction_type = 0 230 self.current_session = current_session.CurrentSession("", "", "") 231 self.is_distance_plot_open = False 232 self.distance_plot_dialog = None 233 234 self.main_window_state = main_window_state.MainWindowState( 235 results_state.ResultsState(), 236 image_state.ImageState(), 237 ) 238 239 constants.PYSSA_LOGGER.info("Setup class attributes finished.") 240 # </editor-fold> 241 242 # sets up the status bar 243 self._setup_statusbar() 244 tools.create_directory(constants.SETTINGS_DIR, "scratch") 245 self._setup_default_configuration() 246 247 # if len(os.listdir(constants.LOG_PATH)) > 0: 248 # self.open_change_log() 249 250 constants.PYSSA_LOGGER.info("Setup rest of GUI related elements ...") 251 252 # <editor-fold desc="GUI page management"> 253 # -- Gui page management vars 254 self.batch_analysis_management: gui_page_management.GuiPageManagement 255 self.results_management: gui_page_management.GuiPageManagement 256 257 # management functions 258 self._create_batch_analysis_management() 259 self._create_results_management() 260 261 # </editor-fold> 262 263 # <editor-fold desc="Block box definitions"> 264 self.block_box_analysis = basic_boxes.no_buttons( 265 "Analysis", 266 "An analysis is currently running, please wait.", 267 QtWidgets.QMessageBox.Information, 268 ) 269 self.block_box_prediction: QtWidgets.QMessageBox = QtWidgets.QMessageBox() 270 self.block_box_images = basic_boxes.no_buttons( 271 "Analysis Images", 272 "Images getting created, please wait.", 273 QtWidgets.QMessageBox.Information, 274 ) 275 self.block_box_uni = basic_boxes.no_buttons("Generic", "Generic", QtWidgets.QMessageBox.Information) 276 277 # </editor-fold> 278 279 # configure gui element properties 280 self._view.ui.txt_results_aligned_residues.setAlignment(QtCore.Qt.AlignRight) 281 self._view.ui.table_pred_mono_prot_to_predict.setSizeAdjustPolicy( 282 QtWidgets.QAbstractScrollArea.AdjustToContents, 283 ) 284 self._view.ui.table_pred_mono_prot_to_predict.horizontalHeader().setDefaultAlignment(QtCore.Qt.AlignLeft) 285 self._view.ui.table_pred_multi_prot_to_predict.horizontalHeader().setDefaultAlignment(QtCore.Qt.AlignLeft) 286 self._view.ui.list_pred_analysis_multi_ref_chains.setSelectionMode( 287 QtWidgets.QAbstractItemView.ExtendedSelection, 288 ) 289 self._view.ui.list_pred_analysis_multi_model_chains.setSelectionMode( 290 QtWidgets.QAbstractItemView.ExtendedSelection, 291 ) 292 293 # helper attributes 294 self.pymol_session_specs = { 295 pyssa_keys.SESSION_SPEC_PROTEIN: [0, ""], 296 pyssa_keys.SESSION_SPEC_COLOR: [0, ""], 297 pyssa_keys.SESSION_SPEC_REPRESENTATION: [0, ""], 298 pyssa_keys.SESSION_SPEC_BG_COLOR: [0, ""], 299 } 300 301 # <editor-fold desc="Setup defaults for pages"> 302 self._init_fill_combo_boxes() 303 self._init_new_page() 304 self._init_use_page() 305 self._init_local_pred_mono_page() 306 self._init_local_pred_multi_page() 307 self._init_batch_analysis_page() 308 self._view.ui.action_toggle_notebook_visibility.setVisible(False) 309 self._view.ui.action_settings_model_w_off_colab_notebook.setVisible(False) 310 self.last_sidebar_button = QtWidgets.QPushButton() 311 self._view.ui.table_pred_mono_prot_to_predict.setEditTriggers( 312 self._view.ui.table_pred_mono_prot_to_predict.NoEditTriggers, 313 ) 314 self._view.ui.table_pred_multi_prot_to_predict.setEditTriggers( 315 self._view.ui.table_pred_multi_prot_to_predict.NoEditTriggers, 316 ) 317 self._view.ui.table_pred_analysis_mono_prot_to_predict.setEditTriggers( 318 self._view.ui.table_pred_analysis_mono_prot_to_predict.NoEditTriggers, 319 ) 320 self._view.ui.table_pred_analysis_multi_prot_to_predict.setEditTriggers( 321 self._view.ui.table_pred_analysis_multi_prot_to_predict.NoEditTriggers, 322 ) 323 324 # TODO: temp gui changes (need to be changed in the designer) 325 self._view.ui.lbl_hotspots_resi_show.setText("Residue(s) as sticks") 326 self._view.ui.lbl_hotspots_resi_hide.setText("Residue(s) as sticks") 327 328 # fixme: should the pdf documentation be accessible through the pyssa gui? 329 self._view.ui.action_help_docs_pdf.setText("Documentation") 330 self._view.ui.action_help_docs_pdf.setVisible(True) 331 self._view.ui.action_help_docs.setText("Tutorials") 332 self._view.ui.action_help_docs.setVisible(True) 333 334 if self._application_settings.wsl_install == 1 and self._application_settings.local_colabfold == 0: 335 self._view.ui.action_install_from_file.setVisible(True) 336 else: 337 self._view.ui.action_install_from_file.setVisible(False) 338 # </editor-fold> 339 340 self._connect_all_gui_elements() 341 342 self._project_watcher.show_valid_options(self._view.ui) 343 self._project_watcher.check_workspace_for_projects(self._workspace_path, self._view.ui) 344 345 self.threadpool = QtCore.QThreadPool() 346 # create scratch and cache dir 347 try: 348 filesystem_helpers.delete_directory(constants.SCRATCH_DIR) 349 except Exception as e: 350 constants.PYSSA_LOGGER.warning(f"Scratch path could not be deleted. {e}") 351 filesystem_helpers.create_directory(constants.SCRATCH_DIR) 352 filesystem_helpers.create_directory(constants.CACHE_DIR)
Constructor.
Arguments:
- a_view: the main view of the pyssa plugin.
Raises:
- IllegalArgumentException: If an argument is illegal.
def
start_worker_thread(self, worker_obj: object, post_process_func) -> None:
354 def start_worker_thread(self, worker_obj: object, post_process_func) -> None: # noqa: ANN001 355 """Sets up the worker, moves the worker to a thread and starts the thread. 356 357 Args: 358 worker_obj: an object of type <work>Worker (QObject). 359 post_process_func: a function which sould be executed if the worker is finished. 360 """ 361 self.tmp_thread = QtCore.QThread() 362 self.tmp_worker = worker_obj 363 self.tmp_thread = task_workers.setup_worker_for_work(self.tmp_thread, self.tmp_worker, post_process_func) 364 self.tmp_thread.start()
Sets up the worker, moves the worker to a thread and starts the thread.
Arguments:
- worker_obj: an object of type
Worker (QObject). - post_process_func: a function which sould be executed if the worker is finished.
def
restore_settings(self) -> None:
782 def restore_settings(self) -> None: 783 """Restores the settings.xml file to the default values.""" 784 out = gui_utils.warning_dialog_restore_settings("Are you sure you want to restore all settings?") 785 if out: 786 tools.restore_default_settings(self._application_settings) 787 self._view.status_bar.showMessage("Settings were successfully restored.") 788 logging.info("Settings were successfully restored.") 789 else: 790 self._view.status_bar.showMessage("Settings were not modified.") 791 logging.info("Settings were not modified.")
Restores the settings.xml file to the default values.
@staticmethod
def
clear_all_log_files() -> None:
797 @staticmethod 798 def clear_all_log_files() -> None: 799 """Clears all log files generated under .pyssa/logs.""" 800 response = basic_boxes.yes_or_no( 801 "Clear log files", 802 "Are you sure you want to delete all log files?", 803 QtWidgets.QMessageBox.Information, 804 ) 805 if response: 806 try: 807 shutil.rmtree(str(constants.LOG_PATH)) 808 except PermissionError: 809 print("The active log file was not deleted.") 810 if len(os.listdir(str(constants.LOG_PATH))) == 1: 811 basic_boxes.ok("Clear log files", "All log files could be deleted.", QtWidgets.QMessageBox.Information) 812 constants.PYSSA_LOGGER.info("All log files were deleted.") 813 else: 814 basic_boxes.ok("Clear log files", "Not all log files could be deleted.", QtWidgets.QMessageBox.Warning) 815 constants.PYSSA_LOGGER.warning("Not all log files were deleted!")
Clears all log files generated under .pyssa/logs.
def
open_settings_global(self) -> None:
818 def open_settings_global(self) -> None: 819 """Opens the dialog for the global settings.""" 820 dialog = dialog_settings_global.DialogSettingsGlobal() 821 dialog.exec_() 822 self._application_settings = self._application_settings.deserialize_settings() 823 globals.g_settings = self._application_settings 824 self._workspace_path = globals.g_settings.workspace_path 825 self._workspace_label = QtWidgets.QLabel(f"Current Workspace: {self._workspace_path}") 826 self._setup_statusbar()
Opens the dialog for the global settings.
def
open_logs(self) -> None:
828 def open_logs(self) -> None: 829 """Opens a file explorer with all log files and can open a log file in the default application.""" 830 file_dialog = QtWidgets.QFileDialog() 831 log_path = str(constants.LOG_PATH) 832 file_dialog.setDirectory(log_path) 833 file_path, _ = file_dialog.getOpenFileName(self._view, "Select a log file to open", "", "LOG File (*.log)") 834 if file_path: 835 os.startfile(file_path)
Opens a file explorer with all log files and can open a log file in the default application.
@staticmethod
def
open_tutorial() -> None:
837 @staticmethod 838 def open_tutorial() -> None: 839 """Opens the official tutorial pdf file.""" 840 tmp_dialog = dialog_tutorial_videos.TutorialVideosDialog() 841 tmp_dialog.exec_()
Opens the official tutorial pdf file.
@staticmethod
def
open_documentation() -> None:
843 @staticmethod 844 def open_documentation() -> None: 845 """Opens the official plugin documentation as PDF.""" 846 os.startfile(constants.DOCS_PATH)
Opens the official plugin documentation as PDF.
@staticmethod
def
open_about() -> None:
848 @staticmethod 849 def open_about() -> None: 850 """Opens the About dialog.""" 851 dialog = dialog_about.DialogAbout() 852 dialog.exec_()
Opens the About dialog.
def
open_page_information(self) -> None:
854 def open_page_information(self) -> None: 855 """Opens the message box, to display extra information based on the page.""" 856 with open( 857 f"{constants.PAGE_HELP_PATHS_DICT[self._view.ui.lbl_page_title.text()]}", 858 "r", 859 encoding="utf-8", 860 ) as file: 861 html_content = file.read() 862 file.close() 863 tmp_dialog = dialog_help.DialogHelp(html_content) 864 tmp_dialog.exec_()
Opens the message box, to display extra information based on the page.
@staticmethod
def
open_release_notes_in_standard_application() -> None:
866 @staticmethod 867 def open_release_notes_in_standard_application() -> None: 868 """Opens the release notes in the default app.""" 869 os.startfile(constants.CHANGELOG_HTML_PATH)
Opens the release notes in the default app.
def
create_new_project(self) -> None:
927 def create_new_project(self) -> None: 928 """Creates a new project with the content of the new page.""" 929 # <editor-fold desc="Checks"> 930 if self._application_settings.wsl_install == 0: 931 basic_boxes.ok( 932 "Create new project", 933 "Please install local colabfold to create a project!", 934 QtWidgets.QMessageBox.Warning, 935 ) 936 return 937 if self._application_settings.local_colabfold == 0: 938 basic_boxes.ok( 939 "Create new project", 940 "Please install local colabfold to create a project!", 941 QtWidgets.QMessageBox.Warning, 942 ) 943 return 944 945 # </editor-fold> 946 947 self._view.wait_spinner.start() 948 an_add_protein_flag: bool = False 949 if self._view.ui.cb_new_add_reference.checkState() == 2: 950 an_add_protein_flag = True 951 952 self._active_task = tasks.Task( 953 target=main_presenter_async.create_new_project, 954 args=( 955 self._view.ui.txt_new_project_name.text(), 956 self._workspace_path, 957 an_add_protein_flag, 958 self._view.ui.txt_new_choose_reference.text(), 959 ), 960 post_func=self.__await_create_new_project, 961 ) 962 self._active_task.start() 963 self.update_status("Creating new project ...")
Creates a new project with the content of the new page.
def
open_project(self) -> None:
988 def open_project(self) -> None: 989 """Initiates the task to open an existing project.""" 990 self._view.wait_spinner.start() 991 self._active_task = tasks.Task( 992 target=main_presenter_async.open_project, 993 args=( 994 self._workspace_path, 995 self._view.ui.txt_open_selected_project.text(), 996 self._application_settings, 997 ), 998 post_func=self.__await_open_project, 999 ) 1000 self._active_task.start() 1001 self.update_status("Opening existing project ...")
Initiates the task to open an existing project.
def
delete_project(self) -> None:
1025 def delete_project(self) -> None: 1026 """Deletes an existing project.""" 1027 # popup message which warns the user that the selected project gets deleted 1028 response: bool = gui_utils.warning_message_project_gets_deleted() 1029 tmp_project_name = self._view.ui.txt_delete_selected_projects.text() 1030 if response is True: 1031 os.remove(pathlib.Path(f"{self._workspace_path}/{self._view.ui.txt_delete_selected_projects.text()}")) 1032 if self._view.ui.txt_delete_selected_projects.text() == self._view.ui.lbl_current_project_name.text(): 1033 self._view.ui.lbl_current_project_name.clear() 1034 self._view.ui.txt_delete_selected_projects.clear() 1035 # update list 1036 self._view.ui.list_delete_projects.clear() 1037 # pre-process 1038 self._view.status_bar.showMessage(self._workspace_label.text()) 1039 self._view.ui.list_delete_projects.clear() 1040 self._view.status_bar.showMessage(self._workspace_label.text()) 1041 tools.scan_workspace_for_valid_projects(self._workspace_path, self._view.ui.list_delete_projects) 1042 constants.PYSSA_LOGGER.info(f"The project {tmp_project_name} was successfully deleted.") 1043 if self._view.ui.list_delete_projects.count() == 0: 1044 self.display_home_page() 1045 self._project_watcher.check_workspace_for_projects(self._workspace_path, self._view.ui) 1046 else: 1047 constants.PYSSA_LOGGER.info("No project has been deleted. No changes were made.")
Deletes an existing project.
def
save_project(self) -> None:
1052 def save_project(self) -> None: 1053 """Saves the project.xml.""" 1054 self._view.wait_spinner.start() 1055 self.last_sidebar_button = styles.color_sidebar_buttons( 1056 self.last_sidebar_button, 1057 self._view.ui.btn_save_project, 1058 ) 1059 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 1060 self._active_task = tasks.Task( 1061 target=main_presenter_async.save_project, 1062 args=(self._current_project, 0), 1063 post_func=self.__await_save_project, 1064 ) 1065 self._active_task.start() 1066 self.update_status("Saving current project ...")
Saves the project.xml.
def
check_for_cleaning(self) -> None:
1076 def check_for_cleaning(self) -> None: 1077 """Checks if the selected protein can be cleaned.""" 1078 self._view.wait_spinner.start() 1079 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 1080 try: 1081 tmp_protein_name: str = self._view.ui.list_edit_project_proteins.currentItem().text() 1082 except AttributeError: 1083 self._view.wait_spinner.stop() 1084 return 1085 self._active_task = tasks.Task( 1086 target=main_presenter_async.check_for_cleaning, 1087 args=( 1088 tmp_protein_name, 1089 self._current_project, 1090 ), 1091 post_func=self.__await_check_for_cleaning, 1092 ) 1093 self._active_task.start() 1094 self.update_status("Checking protein properties ...")
Checks if the selected protein can be cleaned.
def
clean_protein_new(self) -> None:
1138 def clean_protein_new(self) -> None: 1139 """Cleans the selected protein structure and creates a new cleaned structure.""" 1140 self._view.wait_spinner.start() 1141 self._active_task = tasks.Task( 1142 target=main_presenter_async.clean_protein_new, 1143 args=( 1144 self._view.ui.list_edit_project_proteins.currentItem().text().replace(".pdb", ""), 1145 self._current_project, 1146 ), 1147 post_func=self.__await_clean_protein_new, 1148 ) 1149 self._active_task.start() 1150 self.update_status("Duplicating and cleaning protein ...")
Cleans the selected protein structure and creates a new cleaned structure.
def
clean_protein_update(self) -> None:
1158 def clean_protein_update(self) -> None: 1159 """Cleans the selected protein structure.""" 1160 self._view.wait_spinner.start() 1161 if basic_boxes.yes_or_no( 1162 "Clean protein", 1163 "Are you sure you want to clean this protein?\n" "This will remove all organic and solvent components!", 1164 QtWidgets.QMessageBox.Information, 1165 ): 1166 self._active_task = tasks.Task( 1167 target=main_presenter_async.clean_protein_update, 1168 args=( 1169 self._view.ui.list_edit_project_proteins.currentItem().text().replace(".pdb", ""), 1170 self._current_project, 1171 ), 1172 post_func=self.__await_clean_protein_update, 1173 ) 1174 self._active_task.start() 1175 self.update_status("Cleaning protein ...") 1176 else: 1177 constants.PYSSA_LOGGER.info("No protein has been cleaned.") 1178 self._view.wait_spinner.stop()
Cleans the selected protein structure.
def
delete_protein(self) -> None:
1186 def delete_protein(self) -> None: 1187 """Deletes the selected protein structure.""" 1188 self._view.wait_spinner.start() 1189 if gui_utils.warning_message_protein_gets_deleted(): 1190 self._active_task = tasks.Task( 1191 target=main_presenter_async.delete_protein, 1192 args=( 1193 self._view.ui.list_edit_project_proteins.currentItem().text(), 1194 self._current_project, 1195 ), 1196 post_func=self.__await_delete_protein, 1197 ) 1198 self._active_task.start() 1199 self.update_status("Deleting protein ...") 1200 else: 1201 constants.PYSSA_LOGGER.info("No protein was deleted.") 1202 self._view.wait_spinner.stop()
Deletes the selected protein structure.
def
add_existing_protein(self) -> None:
1210 def add_existing_protein(self) -> None: 1211 """Opens a dialog to adds an existing protein structure to the project.""" 1212 self.tmp_dialog = view_add_protein.AddProteinView() 1213 self.tmp_dialog.return_value.connect(self.post_add_existing_protein) 1214 self.tmp_dialog.show()
Opens a dialog to adds an existing protein structure to the project.
def
post_add_existing_protein(self, return_value: tuple) -> None:
1216 def post_add_existing_protein(self, return_value: tuple) -> None: 1217 """Adds an existing protein structure to the current project either by id or from the filesystem. 1218 1219 Args: 1220 return_value: a tuple consisting of the filepath or PDB id and the length of the first one. 1221 """ 1222 self._view.wait_spinner.start() 1223 if return_value[1] > 0: 1224 self._active_task = tasks.Task( 1225 target=main_presenter_async.add_existing_protein_to_project, 1226 args=(return_value, self._current_project), 1227 post_func=self.__await_post_add_existing_protein, 1228 ) 1229 self._active_task.start() 1230 self.update_status("Adding protein to current project ...") 1231 else: 1232 self._view.wait_spinner.stop() 1233 self.display_edit_page()
Adds an existing protein structure to the current project either by id or from the filesystem.
Arguments:
- return_value: a tuple consisting of the filepath or PDB id and the length of the first one.
def
save_selected_protein_structure_as_pdb_file(self) -> None:
1242 def save_selected_protein_structure_as_pdb_file(self) -> None: 1243 """Saves selected protein as pdb file.""" 1244 self._view.wait_spinner.start() 1245 file_dialog = QtWidgets.QFileDialog() 1246 desktop_path = QtCore.QStandardPaths.standardLocations(QtCore.QStandardPaths.DesktopLocation)[0] 1247 file_dialog.setDirectory(desktop_path) 1248 file_path, _ = file_dialog.getSaveFileName( 1249 self._view, 1250 "Save protein structure", 1251 "", 1252 "Protein Data Bank File (*.pdb)", 1253 ) 1254 if file_path: 1255 self._active_task = tasks.Task( 1256 target=main_presenter_async.save_selected_protein_structure_as_pdb_file, 1257 args=(self._view.ui.list_edit_project_proteins.currentItem().text(), self._current_project, file_path), 1258 post_func=self.__await_save_selected_protein_structure_as_pdb_file, 1259 ) 1260 self._active_task.start() 1261 else: 1262 self._view.wait_spinner.stop()
Saves selected protein as pdb file.
def
rename_selected_protein_structure(self) -> None:
1287 def rename_selected_protein_structure(self) -> None: 1288 """Opens a new view to rename the selected protein.""" 1289 self._view.wait_spinner.start() 1290 self.tmp_dialog = dialog_rename_protein.DialogRenameProtein(self._workspace_path) 1291 self.tmp_dialog.return_value.connect(self.post_rename_selected_protein_structure) 1292 self.tmp_dialog.show()
Opens a new view to rename the selected protein.
def
post_rename_selected_protein_structure(self, return_value: tuple) -> None:
1294 def post_rename_selected_protein_structure(self, return_value: tuple) -> None: 1295 """Renames a selected protein structure.""" 1296 if return_value[1] is True: 1297 self._active_task = tasks.Task( 1298 target=main_presenter_async.rename_selected_protein_structure, 1299 args=( 1300 self._view.ui.list_edit_project_proteins.currentItem().text(), 1301 return_value[0], 1302 self._current_project, 1303 ), 1304 post_func=self.__await_post_rename_selected_protein_structure, 1305 ) 1306 self._active_task.start() 1307 else: 1308 self._view.wait_spinner.stop()
Renames a selected protein structure.
def
view_structure(self) -> None:
1318 def view_structure(self) -> None: 1319 """Displays the structure of the selected protein in pymol.""" 1320 protein_name = self._view.ui.list_view_project_proteins.currentItem().text() 1321 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 1322 cmd.reinitialize() 1323 self._view.ui.btn_manage_session.show() 1324 try: 1325 self._current_project.search_protein(protein_name).load_protein_pymol_session() 1326 constants.PYSSA_LOGGER.info("Loaded PyMOL session of protein %s", protein_name) 1327 except pymol.CmdException: 1328 constants.PYSSA_LOGGER.error("Error while loading protein in PyMOL!") 1329 return 1330 self.current_session = current_session.CurrentSession( 1331 "protein", 1332 protein_name, 1333 self._current_project.search_protein(protein_name).pymol_session, 1334 ) 1335 print(self.current_session)
Displays the structure of the selected protein in pymol.
def
display_use_page(self) -> None:
1340 def display_use_page(self) -> None: 1341 """Displays the use project page.""" 1342 self._view.wait_spinner.start() 1343 if self.is_distance_plot_open: 1344 self.distance_plot_dialog.close() 1345 self.is_distance_plot_open = False 1346 1347 self.start_worker_thread( 1348 task_workers.LoadUsePageWorker( 1349 self._workspace_path, 1350 self._current_project.convert_list_of_proteins_to_list_of_protein_infos(), 1351 ), 1352 self.post_display_use_page, 1353 ) 1354 self._init_use_page()
Displays the use project page.
def
post_display_use_page(self, return_value) -> None:
1356 def post_display_use_page(self, return_value) -> None: # noqa: ANN001 1357 """Displays the use project page, after cpu intense task (post thread method). 1358 1359 Args: 1360 return_value: the value which gets returned from the thread process 1361 """ 1362 # this for-loop is necessary for eliminating all proteins which are in the current project from the ones which 1363 # are available 1364 for tmp_item in return_value[0]: 1365 self._view.ui.list_use_available_protein_structures.addItem(tmp_item) 1366 for i in range(self._view.ui.list_use_selected_protein_structures.count()): 1367 self._view.ui.list_use_selected_protein_structures.setCurrentRow(i) 1368 tmp_prot_name = self._view.ui.list_use_selected_protein_structures.currentItem().text() 1369 if tmp_prot_name in return_value[1]: 1370 return_value[1].remove(tmp_prot_name) 1371 1372 for tmp_item in return_value[1]: 1373 self._view.ui.list_use_available_protein_structures.addItem(tmp_item) 1374 for tmp_project_name in return_value[2]: 1375 self._view.ui.list_use_existing_projects.addItem(QtWidgets.QListWidgetItem(tmp_project_name)) 1376 1377 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 14, "Use existing project") 1378 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_use_page) 1379 self._view.wait_spinner.stop()
Displays the use project page, after cpu intense task (post thread method).
Arguments:
- return_value: the value which gets returned from the thread process
def
pre_create_use_project(self) -> None:
1381 def pre_create_use_project(self) -> None: 1382 """Sets up the worker for the create_use_project task.""" 1383 QtWidgets.QApplication.setOverrideCursor(Qt.WaitCursor) 1384 # copy proteins in new project 1385 proteins_to_copy = [] 1386 for i in range(self._view.ui.list_use_selected_protein_structures.count()): 1387 self._view.ui.list_use_selected_protein_structures.setCurrentRow(i) 1388 proteins_to_copy.append(self._view.ui.list_use_selected_protein_structures.currentItem().text()) 1389 1390 # <editor-fold desc="Worker setup"> 1391 # --Begin: worker setup 1392 self.tmp_thread = QtCore.QThread() 1393 self.tmp_worker = task_workers.CreateUseProjectWorker(self._workspace_path, proteins_to_copy) 1394 self.tmp_thread = task_workers.setup_worker_for_work(self.tmp_thread, self.tmp_worker, self.create_use_project) 1395 self.tmp_thread.start() 1396 # --End: worker setup 1397 1398 # </editor-fold> 1399 1400 self._view.ui.lbl_current_project_name.setText(self._view.ui.txt_use_project_name.text()) 1401 self._view.status_bar.showMessage(f"Creating new project: {self._view.ui.txt_use_project_name.text()} ...") 1402 # save project folder in current workspace 1403 new_project = project.Project(self._view.ui.txt_use_project_name.text(), self._workspace_path) 1404 # new_project.create_project_tree() 1405 self._current_project = new_project
Sets up the worker for the create_use_project task.
def
create_use_project(self, proteins_for_new_project) -> None:
1407 def create_use_project(self, proteins_for_new_project) -> None: # noqa: ANN001 1408 """Post thread method. 1409 1410 Args: 1411 proteins_for_new_project (list): the proteins which are in the new project 1412 """ 1413 for tmp_protein_obj in proteins_for_new_project: 1414 self._current_project.add_existing_protein(tmp_protein_obj) 1415 self._current_project.serialize_project( 1416 pathlib.Path(f"{self._workspace_path}/{self._current_project.get_project_name()}.xml"), 1417 ) 1418 # shows options which can be done with the data in the project folder 1419 self._project_watcher.current_project = self._current_project 1420 self._project_watcher.on_home_page = False 1421 self._project_watcher.show_valid_options(self._view.ui) 1422 self.project_scanner.project = self._current_project 1423 self._init_use_page() 1424 constants.PYSSA_LOGGER.info( 1425 f"The project {self._current_project.get_project_name()} was successfully created through a use.", 1426 ) 1427 self.display_view_page() 1428 QtWidgets.QApplication.restoreOverrideCursor()
Post thread method.
Arguments:
- proteins_for_new_project (list): the proteins which are in the new project
def
import_project(self) -> None:
1433 def import_project(self) -> None: 1434 """Imports a project.xml into the current workspace.""" 1435 self.last_sidebar_button = styles.color_sidebar_buttons( 1436 self.last_sidebar_button, 1437 self._view.ui.btn_import_project, 1438 ) 1439 file_dialog = QtWidgets.QFileDialog() 1440 desktop_path = QtCore.QStandardPaths.standardLocations(QtCore.QStandardPaths.DesktopLocation)[0] 1441 file_dialog.setDirectory(desktop_path) 1442 file_path, _ = file_dialog.getOpenFileName( 1443 self._view, 1444 "Select a project file to import", 1445 "", 1446 "XML Files (*.xml)", 1447 ) 1448 if file_path: 1449 tmp_project = project.Project("", self._workspace_path) 1450 tmp_project = tmp_project.deserialize_project(pathlib.Path(file_path), self._application_settings) 1451 tmp_project.set_workspace_path(self._workspace_path) 1452 if len(tmp_project.proteins) <= 1: 1453 if self._application_settings.wsl_install == 0: 1454 basic_boxes.ok( 1455 "Create new project", 1456 "Please install local colabfold to import this project!", 1457 QtWidgets.QMessageBox.Warning, 1458 ) 1459 return 1460 elif self._application_settings.local_colabfold == 0: # noqa: RET505 1461 basic_boxes.ok( 1462 "Create new project", 1463 "Please install local colabfold to import this project!", 1464 QtWidgets.QMessageBox.Warning, 1465 ) 1466 return 1467 new_filepath = pathlib.Path(f"{self._workspace_path}/{tmp_project.get_project_name()}.xml") 1468 tmp_project.serialize_project(new_filepath) 1469 self._current_project = self._current_project.deserialize_project(new_filepath, self._application_settings) 1470 constants.PYSSA_LOGGER.info(f"Opening the project {self._current_project.get_project_name()}.") 1471 self._project_watcher.current_project = self._current_project 1472 self.project_scanner.project = self._current_project 1473 constants.PYSSA_LOGGER.info( 1474 f"{self._project_watcher.current_project.get_project_name()} is the current project.", 1475 ) 1476 self._view.ui.lbl_current_project_name.setText(self._current_project.get_project_name()) 1477 self._project_watcher.on_home_page = False 1478 self._project_watcher.show_valid_options(self._view.ui) 1479 self._view.ui.btn_manage_session.show() 1480 self.display_view_page() 1481 basic_boxes.ok( 1482 "Import Project", 1483 "The project was successfully imported.", 1484 QtWidgets.QMessageBox.Information, 1485 )
Imports a project.xml into the current workspace.
def
export_current_project(self) -> None:
1487 def export_current_project(self) -> None: 1488 """Exports the current project to an importable format.""" 1489 if self.is_distance_plot_open: 1490 self.distance_plot_dialog.close() 1491 self.is_distance_plot_open = False 1492 self.last_sidebar_button = styles.color_sidebar_buttons( 1493 self.last_sidebar_button, 1494 self._view.ui.btn_export_project, 1495 ) 1496 file_dialog = QtWidgets.QFileDialog() 1497 desktop_path = QtCore.QStandardPaths.standardLocations(QtCore.QStandardPaths.DesktopLocation)[0] 1498 file_dialog.setDirectory(desktop_path) 1499 file_path, _ = file_dialog.getSaveFileName(self._view, "Save current project", "", "XML Files (*.xml)") 1500 if file_path: 1501 self._current_project.serialize_project(pathlib.Path(file_path)) 1502 basic_boxes.ok( 1503 "Export Project", 1504 "The project was successfully exported.", 1505 QtWidgets.QMessageBox.Information, 1506 )
Exports the current project to an importable format.
def
close_project(self) -> None:
1511 def close_project(self) -> None: 1512 """Closes the current project.""" 1513 if self.is_distance_plot_open: 1514 self.distance_plot_dialog.close() 1515 self.is_distance_plot_open = False 1516 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 1517 cmd.reinitialize() 1518 self._view.ui.list_hotspots_choose_protein.clear() 1519 self._project_watcher.on_home_page = True 1520 self._project_watcher.current_project = project.Project("", pathlib.Path("")) 1521 self._project_watcher.show_valid_options(self._view.ui) 1522 self._view.ui.lbl_current_project_name.setText("") 1523 self._init_all_pages() 1524 self.results_name = "" 1525 constants.PYSSA_LOGGER.info(f"The project {self._current_project.get_project_name()} was closed") 1526 self.display_home_page()
Closes the current project.
def
post_predict_esm_monomer(self, output) -> None:
1531 def post_predict_esm_monomer(self, output) -> None: # noqa: ANN001 1532 """Post thread method, for the prediction process. 1533 1534 Args: 1535 output (list): the proteins which got predicted 1536 """ 1537 self.block_box_prediction.destroy(True) 1538 for tmp_filename in os.listdir(constants.ESMFOLD_PDB_DIR): 1539 constants.PYSSA_LOGGER.info( 1540 f"Add protein {tmp_filename} to the current project {self._current_project.get_project_name()}", 1541 ) 1542 self._current_project.add_existing_protein( 1543 protein.Protein( 1544 tmp_filename.replace(".pdb", ""), 1545 path_util.FilePath(pathlib.Path(f"{constants.ESMFOLD_PDB_DIR}/{tmp_filename}")), 1546 ), 1547 ) 1548 if len(output) > 0: 1549 formatted_output = ", ".join(output) 1550 basic_boxes.ok( 1551 "ESMFold Prediction", 1552 f"These protein prediction failed: {formatted_output}.", 1553 QtWidgets.QMessageBox.Critical, 1554 ) 1555 else: 1556 basic_boxes.ok("ESMFold Prediction", "The prediction was successful.", QtWidgets.QMessageBox.Information) 1557 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 1558 self.display_view_page() 1559 self._project_watcher.show_valid_options(self._view.ui)
Post thread method, for the prediction process.
Arguments:
- output (list): the proteins which got predicted
def
predict_esm_monomer(self) -> None:
1561 def predict_esm_monomer(self) -> None: 1562 """Sets up the worker to predict the proteins with the ESM-Fold.""" 1563 # <editor-fold desc="Worker setup"> 1564 # --Begin: worker setup 1565 self.tmp_thread = QtCore.QThread() 1566 self.tmp_worker = task_workers.EsmFoldWorker(self._view.ui.table_esm_prot_to_predict) 1567 self.tmp_thread = task_workers.setup_worker_for_work( 1568 self.tmp_thread, 1569 self.tmp_worker, 1570 self.post_predict_esm_monomer, 1571 ) 1572 self.tmp_thread.start() 1573 # --End: worker setup 1574 1575 # </editor-fold> 1576 1577 self.block_box_prediction = QtWidgets.QMessageBox() 1578 self.block_box_prediction = gui_utils.setup_standard_block_box( 1579 self.block_box_prediction, 1580 "Structure Prediction", 1581 "A prediction is currently running.", 1582 ) 1583 # self.block_box_prediction.setStandardButtons(QtWidgets.QMessageBox.NoButton) 1584 # self.block_box_prediction.setIcon(QtWidgets.QMessageBox.Information) 1585 # self.block_box_prediction.setWindowIcon( 1586 # PyQt5.constants.PLUGIN_LOGO_ICON_OBJ) 1587 # styles.set_stylesheet(self.block_box_prediction) 1588 # self.block_box_prediction.setWindowTitle("Structure Prediction") 1589 # self.block_box_prediction.setText("A prediction is currently running.") 1590 self.block_box_prediction.exec_()
Sets up the worker to predict the proteins with the ESM-Fold.
def
post_prediction_process(self, an_exit_code: int, an_exit_code_description: str) -> None:
1595 def post_prediction_process(self, an_exit_code: int, an_exit_code_description: str) -> None: 1596 """Process which runs after each prediction job.""" 1597 if an_exit_code == exit_codes.ERROR_WRITING_FASTA_FILES[0]: 1598 self.block_box_prediction.destroy(True) 1599 basic_boxes.ok( 1600 "Prediction", 1601 "Prediction failed because there was an error writing the fasta file(s)!", 1602 QtWidgets.QMessageBox.Critical, 1603 ) 1604 self.display_view_page() 1605 self._project_watcher.show_valid_options(self._view.ui) 1606 constants.PYSSA_LOGGER.error(f"Prediction ended with exit code {an_exit_code}: {an_exit_code_description}") 1607 elif an_exit_code == exit_codes.ERROR_FASTA_FILES_NOT_FOUND[0]: 1608 self.block_box_prediction.destroy(True) 1609 basic_boxes.ok( 1610 "Prediction", 1611 "Prediction failed because the fasta file(s) could not be found!", 1612 QtWidgets.QMessageBox.Critical, 1613 ) 1614 self.display_view_page() 1615 self._project_watcher.show_valid_options(self._view.ui) 1616 constants.PYSSA_LOGGER.error(f"Prediction ended with exit code {an_exit_code}: {an_exit_code_description}") 1617 elif an_exit_code == exit_codes.ERROR_PREDICTION_FAILED[0]: 1618 self.block_box_prediction.destroy(True) 1619 basic_boxes.ok( 1620 "Prediction", 1621 "Prediction failed because a subprocess failed!", 1622 QtWidgets.QMessageBox.Critical, 1623 ) 1624 self.display_view_page() 1625 self._project_watcher.show_valid_options(self._view.ui) 1626 constants.PYSSA_LOGGER.error(f"Prediction ended with exit code {an_exit_code}: {an_exit_code_description}") 1627 elif an_exit_code == exit_codes.EXIT_CODE_ONE_UNKNOWN_ERROR[0]: 1628 self.block_box_prediction.destroy(True) 1629 basic_boxes.ok( 1630 "Prediction", 1631 "Prediction failed because of an unknown error!", 1632 QtWidgets.QMessageBox.Critical, 1633 ) 1634 self.display_view_page() 1635 self._project_watcher.show_valid_options(self._view.ui) 1636 constants.PYSSA_LOGGER.error(f"Prediction ended with exit code {an_exit_code}: {an_exit_code_description}") 1637 elif an_exit_code == exit_codes.EXIT_CODE_ZERO[0]: 1638 # Prediction was successful 1639 if self.prediction_type == constants.PREDICTION_TYPE_PRED: 1640 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 1641 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 1642 self.block_box_prediction.destroy(True) 1643 basic_boxes.ok( 1644 "Structure prediction", 1645 "All structure predictions are done. Go to View to check the new proteins.", 1646 QtWidgets.QMessageBox.Information, 1647 ) 1648 constants.PYSSA_LOGGER.info("All structure predictions are done.") 1649 self._project_watcher.show_valid_options(self._view.ui) 1650 self._init_local_pred_mono_page() 1651 self._init_local_pred_multi_page() 1652 self.display_view_page() 1653 elif self.prediction_type == constants.PREDICTION_TYPE_PRED_MONO_ANALYSIS: 1654 # executes if monomers were successfully predicted 1655 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 1656 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 1657 constants.PYSSA_LOGGER.info("All structure predictions are done.") 1658 constants.PYSSA_LOGGER.info("Begin analysis process.") 1659 constants.PYSSA_LOGGER.debug( 1660 f"Thread count before analysis worker: {self.threadpool.activeThreadCount()}", 1661 ) 1662 1663 # self.worker_analysis = workers.AnalysisWorkerPool( 1664 # self._view.ui.list_pred_analysis_mono_overview, self._view.ui.cb_pred_analysis_mono_images, 1665 # self._view.status_bar, self._current_project, self._application_settings, self._init_mono_pred_analysis_page) 1666 constants.PYSSA_LOGGER.info("Thread started for analysis process.") 1667 # self.threadpool.start(self.worker_analysis) 1668 constants.PYSSA_LOGGER.debug( 1669 f"Thread count after analysis worker: {self.threadpool.activeThreadCount()}", 1670 ) 1671 1672 # <editor-fold desc="Worker setup"> 1673 # TODO: test code below 1674 # --Begin: worker setup 1675 self.tmp_thread = QtCore.QThread() 1676 self.tmp_worker = task_workers.DistanceAnalysisWorker( 1677 self._view.ui.list_pred_analysis_mono_overview, 1678 self._view.ui.cb_pred_analysis_mono_images, 1679 self._view.status_bar, 1680 self._current_project, 1681 self._application_settings, 1682 self._init_mono_pred_analysis_page, 1683 ) 1684 self.tmp_thread = task_workers.setup_worker_for_work( 1685 self.tmp_thread, 1686 self.tmp_worker, 1687 self.display_view_page, 1688 ) 1689 self.tmp_worker.finished.connect(self.post_analysis_process) 1690 self.tmp_thread.start() 1691 # --End: worker setup 1692 1693 # </editor-fold> 1694 1695 if not os.path.exists(constants.SCRATCH_DIR_ANALYSIS): 1696 os.mkdir(constants.SCRATCH_DIR_ANALYSIS) 1697 self.block_box_prediction.destroy(True) 1698 self.block_box_analysis.exec_() 1699 self.display_view_page() 1700 self._project_watcher.show_valid_options(self._view.ui) 1701 elif self.prediction_type == constants.PREDICTION_TYPE_PRED_MULTI_ANALYSIS: 1702 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 1703 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 1704 constants.PYSSA_LOGGER.info("All structure predictions are done.") 1705 constants.PYSSA_LOGGER.info("Begin analysis process.") 1706 constants.PYSSA_LOGGER.debug( 1707 f"Thread count before analysis worker: {self.threadpool.activeThreadCount()}", 1708 ) 1709 1710 # self.worker_analysis = workers.AnalysisWorkerPool( 1711 # self._view.ui.list_pred_analysis_multi_overview, self._view.ui.cb_pred_analysis_multi_images, 1712 # self._view.status_bar, self._current_project, self._application_settings, self._init_multi_pred_analysis_page) 1713 constants.PYSSA_LOGGER.info("Thread started for analysis process.") 1714 # self.threadpool.start(self.worker_analysis) 1715 constants.PYSSA_LOGGER.debug( 1716 f"Thread count after analysis worker: {self.threadpool.activeThreadCount()}", 1717 ) 1718 1719 # <editor-fold desc="Worker setup"> 1720 # TODO: test code below 1721 # --Begin: worker setup 1722 self.tmp_thread = QtCore.QThread() 1723 self.tmp_worker = task_workers.DistanceAnalysisWorker( 1724 self._view.ui.list_pred_analysis_multi_overview, 1725 self._view.ui.cb_pred_analysis_multi_images, 1726 self._view.status_bar, 1727 self._current_project, 1728 self._application_settings, 1729 self._init_multi_pred_analysis_page, 1730 ) 1731 self.tmp_thread = task_workers.setup_worker_for_work( 1732 self.tmp_thread, 1733 self.tmp_worker, 1734 self.display_view_page, 1735 ) 1736 self.tmp_worker.finished.connect(self.post_analysis_process) 1737 self.tmp_thread.start() 1738 # --End: worker setup 1739 1740 # </editor-fold> 1741 1742 if not os.path.exists(constants.SCRATCH_DIR_ANALYSIS): 1743 os.mkdir(constants.SCRATCH_DIR_ANALYSIS) 1744 self.block_box_prediction.destroy(True) 1745 self.block_box_analysis.exec_() 1746 self.display_view_page() 1747 self._project_watcher.show_valid_options(self._view.ui) 1748 try: 1749 shutil.rmtree(pathlib.Path(f"{constants.SCRATCH_DIR}/local_predictions")) 1750 except Exception as e: 1751 constants.PYSSA_LOGGER.warning(f"Local predictions scratch path could not be deleted. {e}")
Process which runs after each prediction job.
def
predict_local_monomer(self) -> None:
1753 def predict_local_monomer(self) -> None: 1754 """Sets tup the worker for the prediction with the colabfold.""" 1755 self._view.wait_spinner.start() 1756 self.prediction_type = constants.PREDICTION_TYPE_PRED 1757 constants.PYSSA_LOGGER.info("Begin prediction process.") 1758 self.update_status("Begin prediction process ...") 1759 predictions: list[ 1760 prediction_protein_info.PredictionProteinInfo 1761 ] = prediction_util.get_prediction_name_and_seq_from_table(self._view.ui.table_pred_mono_prot_to_predict) 1762 1763 self._active_task = tasks.Task( 1764 target=main_presenter_async.predict_protein_with_colabfold, 1765 args=( 1766 predictions, 1767 self.prediction_configuration, 1768 self._current_project, 1769 ), 1770 post_func=self.__await_predict_protein_with_colabfold, 1771 ) 1772 self._active_task.start() 1773 1774 self.block_box_prediction = QtWidgets.QMessageBox() 1775 self.block_box_prediction.setIcon(QtWidgets.QMessageBox.Information) 1776 self.block_box_prediction.setWindowIcon(QtGui.QIcon(constants.PLUGIN_LOGO_FILEPATH)) 1777 styles.set_stylesheet(self.block_box_prediction) 1778 self.block_box_prediction.setWindowTitle("Structure Prediction") 1779 self.block_box_prediction.setText("A prediction is currently running.") 1780 btn_abort = self.block_box_prediction.addButton("Abort", QtWidgets.QMessageBox.ActionRole) 1781 self.block_box_prediction.exec_() 1782 if self.block_box_prediction.clickedButton() == btn_abort: 1783 self.abort_prediction() 1784 self.block_box_prediction.close() 1785 self._view.wait_spinner.stop() 1786 return 1787 else: # noqa: RET505 1788 self.block_box_prediction.close() 1789 self._view.wait_spinner.stop()
Sets tup the worker for the prediction with the colabfold.
def
abort_prediction(self) -> None:
1861 def abort_prediction(self) -> None: 1862 """Aborts the running prediction.""" 1863 constants.PYSSA_LOGGER.info("Structure prediction process was aborted manually.") 1864 subprocess.run(["wsl", "--shutdown"]) 1865 constants.PYSSA_LOGGER.info("Shutdown of wsl environment.") 1866 filesystem_io.FilesystemCleaner.clean_prediction_scratch_folder() 1867 constants.PYSSA_LOGGER.info("Cleaned scratch directory.") 1868 basic_boxes.ok("Abort prediction", "The structure prediction was aborted.", QtWidgets.QMessageBox.Information) 1869 self.last_sidebar_button = styles.color_sidebar_buttons( 1870 self.last_sidebar_button, 1871 self._view.ui.btn_prediction_abort, 1872 ) 1873 self._project_watcher.show_valid_options(self._view.ui)
Aborts the running prediction.
def
predict_local_multimer(self) -> None:
1878 def predict_local_multimer(self) -> None: 1879 """Sets up the worker for the prediction with the colabfold.""" 1880 self._view.wait_spinner.start() 1881 self.prediction_type = constants.PREDICTION_TYPE_PRED 1882 constants.PYSSA_LOGGER.info("Begin multimer prediction process.") 1883 self.update_status("Begin prediction process ...") 1884 predictions: list[ 1885 prediction_protein_info.PredictionProteinInfo 1886 ] = prediction_util.get_prediction_name_and_seq_from_table(self._view.ui.table_pred_multi_prot_to_predict) 1887 1888 self._active_task = tasks.Task( 1889 target=main_presenter_async.predict_protein_with_colabfold, 1890 args=( 1891 predictions, 1892 self.prediction_configuration, 1893 self._current_project, 1894 ), 1895 post_func=self.__await_predict_protein_with_colabfold, 1896 ) 1897 self._active_task.start() 1898 1899 self.block_box_prediction = QtWidgets.QMessageBox() 1900 self.block_box_prediction.setIcon(QtWidgets.QMessageBox.Information) 1901 self.block_box_prediction.setWindowIcon(QtGui.QIcon(constants.PLUGIN_LOGO_FILEPATH)) 1902 styles.set_stylesheet(self.block_box_prediction) 1903 self.block_box_prediction.setWindowTitle("Structure Prediction") 1904 self.block_box_prediction.setText("A prediction is currently running.") 1905 btn_abort = self.block_box_prediction.addButton("Abort", QtWidgets.QMessageBox.ActionRole) 1906 self.block_box_prediction.exec_() 1907 if self.block_box_prediction.clickedButton() == btn_abort: 1908 self.abort_prediction() 1909 self.block_box_prediction.close() 1910 self._view.wait_spinner.stop() 1911 else: 1912 self.block_box_prediction.close() 1913 self._view.wait_spinner.stop()
Sets up the worker for the prediction with the colabfold.
def
start_monomer_prediction_analysis(self) -> None:
1918 def start_monomer_prediction_analysis(self) -> None: 1919 """Sets up the worker for the prediction of the proteins.""" 1920 self._view.wait_spinner.start() 1921 self.prediction_type = constants.PREDICTION_TYPE_PRED_MONO_ANALYSIS 1922 constants.PYSSA_LOGGER.info("Begin prediction process.") 1923 self.update_status("Begin prediction process ...") 1924 predictions: list[ 1925 prediction_protein_info.PredictionProteinInfo 1926 ] = prediction_util.get_prediction_name_and_seq_from_table( 1927 self._view.ui.table_pred_analysis_mono_prot_to_predict, 1928 ) 1929 1930 self._active_task = tasks.Task( 1931 target=main_presenter_async.predict_protein_with_colabfold, 1932 args=( 1933 predictions, 1934 self.prediction_configuration, 1935 self._current_project, 1936 ), 1937 post_func=self.__await_monomer_prediction_for_subsequent_analysis, 1938 ) 1939 self._active_task.start() 1940 1941 self.block_box_prediction = QtWidgets.QMessageBox() 1942 self.block_box_prediction.setIcon(QtWidgets.QMessageBox.Information) 1943 self.block_box_prediction.setWindowIcon(QtGui.QIcon(constants.PLUGIN_LOGO_FILEPATH)) 1944 styles.set_stylesheet(self.block_box_prediction) 1945 self.block_box_prediction.setWindowTitle("Structure Prediction") 1946 self.block_box_prediction.setText("A prediction is currently running.") 1947 btn_abort = self.block_box_prediction.addButton("Abort", QtWidgets.QMessageBox.ActionRole) 1948 self.block_box_prediction.exec_() 1949 if self.block_box_prediction.clickedButton() == btn_abort: 1950 self.abort_prediction() 1951 self.block_box_prediction.close() 1952 self._view.wait_spinner.stop() 1953 else: 1954 self.block_box_prediction.close() 1955 self._view.wait_spinner.stop()
Sets up the worker for the prediction of the proteins.
def
mono_pred_analysis_structure_analysis_next_2(self) -> None:
2042 def mono_pred_analysis_structure_analysis_next_2(self) -> None: 2043 """Shows the gui elements for the chain selection of protein 1.""" 2044 self._view.wait_spinner.start() 2045 tmp_proteins_to_predict: list[str] = [] 2046 for i in range(self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount()): 2047 tmp_proteins_to_predict.append( 2048 self._view.ui.table_pred_analysis_mono_prot_to_predict.verticalHeaderItem(i).text(), 2049 ) 2050 self._active_task = tasks.Task( 2051 target=main_presenter_async.check_chains_for_subsequent_analysis, 2052 args=( 2053 self._view.ui.box_pred_analysis_mono_prot_struct_1.currentText(), 2054 self._view.ui.box_pred_analysis_mono_prot_struct_2.currentText(), 2055 self._current_project, 2056 tmp_proteins_to_predict, 2057 ), 2058 post_func=self.__await_mono_pred_analysis_structure_analysis_next_2, 2059 ) 2060 self._active_task.start()
Shows the gui elements for the chain selection of protein 1.
def
start_multimer_prediction_analysis(self) -> None:
2165 def start_multimer_prediction_analysis(self) -> None: 2166 """Sets up the prediction process.""" 2167 self._view.wait_spinner.start() 2168 self.prediction_type = constants.PREDICTION_TYPE_PRED_MULTI_ANALYSIS 2169 constants.PYSSA_LOGGER.info("Begin prediction process.") 2170 self.update_status("Begin prediction process ...") 2171 predictions: list[ 2172 prediction_protein_info.PredictionProteinInfo 2173 ] = prediction_util.get_prediction_name_and_seq_from_table( 2174 self._view.ui.table_pred_analysis_multi_prot_to_predict, 2175 ) 2176 2177 self._active_task = tasks.Task( 2178 target=main_presenter_async.predict_protein_with_colabfold, 2179 args=( 2180 predictions, 2181 self.prediction_configuration, 2182 self._current_project, 2183 ), 2184 post_func=self.__await_multimer_prediction_for_subsequent_analysis, 2185 ) 2186 self._active_task.start() 2187 2188 self.block_box_prediction = QtWidgets.QMessageBox() 2189 self.block_box_prediction.setIcon(QtWidgets.QMessageBox.Information) 2190 self.block_box_prediction.setWindowIcon(QtGui.QIcon(constants.PLUGIN_LOGO_FILEPATH)) 2191 styles.set_stylesheet(self.block_box_prediction) 2192 self.block_box_prediction.setWindowTitle("Structure Prediction") 2193 self.block_box_prediction.setText("A prediction is currently running.") 2194 btn_abort = self.block_box_prediction.addButton("Abort", QtWidgets.QMessageBox.ActionRole) 2195 self.block_box_prediction.exec_() 2196 if self.block_box_prediction.clickedButton() == btn_abort: 2197 self.abort_prediction() 2198 self.block_box_prediction.close() 2199 self._view.wait_spinner.stop() 2200 else: 2201 self.block_box_prediction.close() 2202 self._view.wait_spinner.stop()
Sets up the prediction process.
def
multi_pred_analysis_structure_analysis_next_2(self) -> None:
2288 def multi_pred_analysis_structure_analysis_next_2(self) -> None: 2289 """Shows the gui elements to select the chains in protein 1.""" 2290 self._view.wait_spinner.start() 2291 tmp_proteins_to_predict: list[str] = [] 2292 for i in range(self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount()): 2293 tmp_proteins_to_predict.append( 2294 self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem(i).text(), 2295 ) 2296 self._active_task = tasks.Task( 2297 target=main_presenter_async.check_chains_for_subsequent_analysis, 2298 args=( 2299 self._view.ui.box_pred_analysis_multi_prot_struct_1.currentText(), 2300 self._view.ui.box_pred_analysis_multi_prot_struct_2.currentText(), 2301 self._current_project, 2302 tmp_proteins_to_predict, 2303 ), 2304 post_func=self.__await_multi_pred_analysis_structure_analysis_next_2, 2305 ) 2306 self._active_task.start()
Shows the gui elements to select the chains in protein 1.
def
post_analysis_process(self, an_exit_code: tuple[int, str]) -> None:
2412 def post_analysis_process(self, an_exit_code: tuple[int, str]) -> None: 2413 """Post process after the analysis thread finished.""" 2414 constants.PYSSA_LOGGER.debug("post_analysis_process() started ...") 2415 if an_exit_code[0] == exit_codes.ERROR_DISTANCE_ANALYSIS_FAILED[0]: 2416 self.block_box_analysis.destroy(True) 2417 basic_boxes.ok( 2418 "Distance analysis", 2419 "Distance analysis failed because there was an error during the analysis!", 2420 QtWidgets.QMessageBox.Critical, 2421 ) 2422 constants.PYSSA_LOGGER.error( 2423 f"Distance analysis ended with exit code {an_exit_code[0]}: {an_exit_code[1]}", 2424 ) 2425 elif an_exit_code[0] == exit_codes.EXIT_CODE_ONE_UNKNOWN_ERROR[0]: 2426 self.block_box_analysis.destroy(True) 2427 basic_boxes.ok( 2428 "Distance analysis", 2429 "Distance analysis failed because of an unknown error!", 2430 QtWidgets.QMessageBox.Critical, 2431 ) 2432 constants.PYSSA_LOGGER.error( 2433 f"Distance analysis ended with exit code {an_exit_code[0]}: {an_exit_code[1]}", 2434 ) 2435 elif an_exit_code[0] == exit_codes.EXIT_CODE_ZERO[0]: 2436 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 2437 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 2438 self.block_box_analysis.destroy(True) 2439 basic_boxes.ok( 2440 "Structure analysis", 2441 "All structure analysis' are done. Go to results to check the new results.", 2442 QtWidgets.QMessageBox.Information, 2443 ) 2444 constants.PYSSA_LOGGER.info("All structure analysis' are done.") 2445 2446 self._project_watcher.show_valid_options(self._view.ui) 2447 self.display_view_page() 2448 self._init_batch_analysis_page()
Post process after the analysis thread finished.
def
start_process_batch(self) -> None:
2450 def start_process_batch(self) -> None: 2451 """Sets up the worker for the analysis task.""" 2452 constants.PYSSA_LOGGER.info("Begin analysis process.") 2453 2454 tmp_raw_analysis_run_names: list = [] 2455 for row_no in range(self._view.ui.list_analysis_batch_overview.count()): 2456 tmp_raw_analysis_run_names.append(self._view.ui.list_analysis_batch_overview.item(row_no).text()) 2457 self._active_task = tasks.Task( 2458 target=main_presenter_async.run_distance_analysis, 2459 args=( 2460 tmp_raw_analysis_run_names, 2461 self._current_project, 2462 self._application_settings, 2463 self._view.ui.cb_analysis_images.isChecked(), 2464 ), 2465 post_func=self.post_analysis_process, 2466 ) 2467 self._active_task.start() 2468 2469 if not os.path.exists(constants.SCRATCH_DIR_ANALYSIS): 2470 os.mkdir(constants.SCRATCH_DIR_ANALYSIS) 2471 2472 self.block_box_analysis.exec_() 2473 self.display_view_page()
Sets up the worker for the analysis task.
def
structure_analysis_next(self) -> None:
2475 def structure_analysis_next(self) -> None: 2476 """Shows the gui elements to select the chains in protein 1.""" 2477 self._view.wait_spinner.start() 2478 self._active_task = tasks.Task( 2479 target=main_presenter_async.check_chains_for_analysis, 2480 args=( 2481 self._view.ui.box_analysis_batch_prot_struct_1.currentText(), 2482 self._view.ui.box_analysis_batch_prot_struct_2.currentText(), 2483 self._current_project, 2484 ), 2485 post_func=self.__await_structure_analysis_next, 2486 ) 2487 self._active_task.start()
Shows the gui elements to select the chains in protein 1.
def
post_image_creation_process(self) -> None:
2580 def post_image_creation_process(self) -> None: 2581 """Post method after the image creation task is finished.""" 2582 self._current_project.serialize_project(self._current_project.get_project_xml_path()) 2583 constants.PYSSA_LOGGER.info("Project has been saved to XML file.") 2584 self.block_box_images.destroy(True) 2585 basic_boxes.ok( 2586 "Analysis Images", 2587 "All images of all analysis' have been created. Go to results to check the new results.", 2588 QtWidgets.QMessageBox.Information, 2589 ) 2590 constants.PYSSA_LOGGER.info("All images of all analysis' have been created.") 2591 self._init_analysis_image_page() 2592 self.display_view_page() 2593 self._project_watcher.show_valid_options(self._view.ui)
Post method after the image creation task is finished.
def
start_automatic_image_creation(self) -> None:
2595 def start_automatic_image_creation(self) -> None: 2596 """Sets up the worker for the image creation process.""" 2597 constants.PYSSA_LOGGER.info("Begin image creation process.") 2598 # self.worker_image_creation = workers.BatchImageWorkerPool( 2599 # self._view.ui.list_analysis_images_struct_analysis, self._view.ui.list_analysis_images_creation_struct_analysis, 2600 # self._view.status_bar, self._current_project) 2601 constants.PYSSA_LOGGER.info("Thread started for image creation process.") 2602 # self.threadpool.start(self.worker_image_creation) 2603 2604 # <editor-fold desc="Worker setup"> 2605 # TODO: test code below 2606 # --Begin: worker setup 2607 self.tmp_thread = QtCore.QThread() 2608 self.tmp_worker = task_workers.BatchImageWorker( 2609 self._view.ui.list_analysis_images_struct_analysis, 2610 self._view.ui.list_analysis_images_creation_struct_analysis, 2611 self._view.status_bar, 2612 self._current_project, 2613 ) 2614 self.tmp_thread = task_workers.setup_worker_for_work(self.tmp_thread, self.tmp_worker, self.display_view_page) 2615 self.tmp_worker.finished.connect(self.post_image_creation_process) 2616 self.tmp_thread.start() 2617 # --End: worker setup 2618 2619 # </editor-fold> 2620 2621 if not os.path.exists(constants.SCRATCH_DIR_ANALYSIS): 2622 os.mkdir(constants.SCRATCH_DIR_ANALYSIS) 2623 2624 self._view.ui.list_analysis_images_struct_analysis.setEnabled(False) 2625 self._view.ui.list_analysis_images_creation_struct_analysis.setEnabled(False) 2626 2627 # gui_elements_to_show = [ 2628 # self._view.ui.btn_analysis_abort, 2629 # ] 2630 # gui_elements_to_hide = [ 2631 # self._view.ui.btn_save_project, 2632 # self._view.ui.btn_edit_page, 2633 # self._view.ui.btn_view_page, 2634 # self._view.ui.btn_use_page, 2635 # self._view.ui.btn_export_project, 2636 # self._view.ui.btn_close_project, 2637 # self._view.ui.btn_batch_analysis_page, 2638 # self._view.ui.btn_image_analysis_page, 2639 # self._view.ui.btn_results_page, 2640 # self._view.ui.lbl_handle_pymol_session, 2641 # self._view.ui.btn_image_page, 2642 # self._view.ui.btn_hotspots_page, 2643 # ] 2644 # gui_utils.manage_gui_visibility(gui_elements_to_show, gui_elements_to_hide) 2645 2646 self.block_box_images.exec_()
Sets up the worker for the image creation process.
def
show_analysis_results_options(self) -> None:
2651 def show_analysis_results_options(self) -> None: 2652 """Shows the combo box of protein pairs.""" 2653 self.results_management.show_stage_x(0)
Shows the combo box of protein pairs.
def
show_results_interactions( self, gui_elements_to_show: list = None, gui_elements_to_hide: list = None) -> None:
2655 def show_results_interactions(self, gui_elements_to_show: list = None, gui_elements_to_hide: list = None) -> None: 2656 """Shows the gui elements of the results page. 2657 2658 Args: 2659 gui_elements_to_show: a list of gui elements which should get displayed. 2660 gui_elements_to_hide: a list of gui elements which should get hidden. 2661 """ 2662 if gui_elements_to_hide is not None: 2663 self.results_management.show_gui_elements_stage_x( 2664 [0, 1], 2665 [], 2666 show_specific_elements=[ 2667 self._view.ui.lbl_results_analysis_options, 2668 self._view.ui.cb_results_analysis_options, 2669 ], 2670 hide_specific_elements=gui_elements_to_hide, 2671 ) 2672 else: 2673 self.results_management.show_gui_elements_stage_x( 2674 [0, 1], 2675 [], 2676 show_specific_elements=[ 2677 self._view.ui.lbl_results_analysis_options, 2678 self._view.ui.cb_results_analysis_options, 2679 ], 2680 )
Shows the gui elements of the results page.
Arguments:
- gui_elements_to_show: a list of gui elements which should get displayed.
- gui_elements_to_hide: a list of gui elements which should get hidden.
def
load_results(self) -> None:
2682 def load_results(self) -> None: 2683 """Sets up the worker for the result loading process.""" 2684 self._view.wait_spinner.start() 2685 if self.is_distance_plot_open: 2686 self.distance_plot_dialog.close() 2687 self.is_distance_plot_open = False 2688 self.results_name = self._view.ui.cb_results_analysis_options.currentText() 2689 if self.results_name == "": 2690 self.show_analysis_results_options() 2691 self._view.wait_spinner.stop() 2692 return 2693 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 2694 2695 self._active_task = tasks.Task( 2696 target=main_presenter_async.load_results, 2697 args=( 2698 self._current_project, 2699 self.results_name, 2700 ), 2701 post_func=self.__await_load_results, 2702 ) 2703 self._active_task.start() 2704 2705 self._view.ui.list_results_interest_regions.clear() 2706 self._view.status_bar.showMessage(f"Loading results of {self.results_name} ...")
Sets up the worker for the result loading process.
def
color_protein_pair_by_rmsd(self) -> None:
2799 def color_protein_pair_by_rmsd(self) -> None: 2800 """Colors the residues in 5 colors depending on their distance to the reference.""" 2801 self._view.wait_spinner.start() 2802 self._active_task = tasks.Task( 2803 target=main_presenter_async.color_protein_pair_by_rmsd_value, 2804 args=( 2805 self._current_project, 2806 self.results_name, 2807 ), 2808 post_func=self.__await_color_protein_pair_by_rmsd, 2809 ) 2810 self._active_task.start() 2811 self._view.status_bar.showMessage("Coloring protein pair by RMSD value ...") 2812 # hide unnecessary representations 2813 # fixme: it might be a problem to hide any representation at this point 2814 # cmd.hide("cartoon", tmp_protein_pair.protein_1.get_molecule_object()) 2815 # cmd.hide("cartoon", f"{tmp_protein_pair.protein_2.get_molecule_object()}") 2816 # cmd.hide("cartoon", f"{tmp_protein_pair.protein_2.get_molecule_object()}")
Colors the residues in 5 colors depending on their distance to the reference.
def
display_structure_alignment(self) -> None:
2824 def display_structure_alignment(self) -> None: 2825 """Opens a window which displays the image of the structure alignment.""" 2826 png_dialog = QtWidgets.QDialog(self._view) 2827 label = QtWidgets.QLabel(self._view) 2828 pathlib.Path( 2829 f"{self._workspace_path}/{self._view.ui.lbl_current_project_name.text()}/results/{self.results_name}", 2830 ) 2831 self._view.ui.cb_results_analysis_options.currentText() 2832 pixmap = QtGui.QPixmap( 2833 f"{constants.CACHE_STRUCTURE_ALN_IMAGES_DIR}/structure_aln_{self._view.ui.cb_results_analysis_options.currentText()}", 2834 ) 2835 # TO-DO: Create setting for min. image size 2836 pixmap = pixmap.scaled(450, 450, transformMode=QtCore.Qt.SmoothTransformation) 2837 label.setPixmap(pixmap) 2838 label.setScaledContents(True) 2839 png_dialog_layout = QtWidgets.QHBoxLayout() 2840 png_dialog_layout.addWidget(label) 2841 png_dialog.setLayout(png_dialog_layout) 2842 png_dialog.setWindowTitle("Image of: structure alignment") 2843 png_dialog.show()
Opens a window which displays the image of the structure alignment.
def
display_distance_plot(self) -> None:
2845 def display_distance_plot(self) -> None: 2846 """Opens a window which displays the distance plot.""" 2847 protein_pair_of_analysis = self._current_project.search_protein_pair( 2848 self._view.ui.cb_results_analysis_options.currentText(), 2849 ) 2850 2851 tmp_dialog = plot_view.PlotView(protein_pair_of_analysis, self._current_project, self._view.ui.cb_results_analysis_options.currentText()) 2852 tmp_dialog.exec_() 2853 2854 # self.distance_plot_dialog = dialog_distance_plot.DialogDistancePlot(protein_pair_of_analysis, self._current_project, 2855 # self._view.ui.cb_results_analysis_options.currentText()) 2856 # self.distance_plot_dialog.setWindowModality(Qt.WindowModal) 2857 # self.is_distance_plot_open = True 2858 # self.distance_plot_dialog.exec_()
Opens a window which displays the distance plot.
def
display_distance_histogram(self) -> None:
2860 def display_distance_histogram(self) -> None: 2861 """Opens a window which displays the distance histogram.""" 2862 if self.is_distance_plot_open: 2863 self.distance_plot_dialog.close() 2864 self.is_distance_plot_open = False 2865 protein_pair_of_analysis = self._current_project.search_protein_pair( 2866 self._view.ui.cb_results_analysis_options.currentText(), 2867 ) 2868 dialog = dialog_distance_histogram.DialogDistanceHistogram(protein_pair_of_analysis) 2869 dialog.exec_()
Opens a window which displays the distance histogram.
def
display_interesting_region(self) -> None:
2871 def display_interesting_region(self) -> None: 2872 """Displays an image of an interesting region.""" 2873 if self.is_distance_plot_open: 2874 self.distance_plot_dialog.close() 2875 self.is_distance_plot_open = False 2876 png_dialog = QtWidgets.QDialog(self._view) 2877 label = QtWidgets.QLabel(self._view) 2878 file_name = self._view.ui.list_results_interest_regions.currentItem().text() 2879 pixmap = QtGui.QPixmap(f"{constants.CACHE_STRUCTURE_ALN_IMAGES_INTERESTING_REGIONS_DIR}/{file_name}") 2880 # TODO: Create setting for min. image size 2881 pixmap = pixmap.scaled(450, 450, transformMode=QtCore.Qt.SmoothTransformation) 2882 label.setPixmap(pixmap) 2883 label.setScaledContents(True) 2884 png_dialog_layout = QtWidgets.QHBoxLayout() 2885 png_dialog_layout.addWidget(label) 2886 png_dialog.setLayout(png_dialog_layout) 2887 png_dialog.setWindowTitle(f"Image of: {file_name}") 2888 png_dialog.show()
Displays an image of an interesting region.
def
display_distance_table(self) -> None:
2890 def display_distance_table(self) -> None: 2891 """Displays the distances in a table.""" 2892 if self.is_distance_plot_open: 2893 self.distance_plot_dialog.close() 2894 self.is_distance_plot_open = False 2895 csv_model = QtGui.QStandardItemModel() 2896 csv_model.setColumnCount(7) 2897 labels = [ 2898 "Residue pair no.", 2899 "Protein 1 Chain", 2900 "Protein 1 Position", 2901 "Protein 1 Residue", 2902 "Protein 2 Chain", 2903 "Protein 2 Position", 2904 "Protein 2 Residue", 2905 "Distance in Å", 2906 ] 2907 csv_model.setHorizontalHeaderLabels(labels) 2908 table_dialog = QtWidgets.QDialog(self._view) 2909 table_view = QtWidgets.QTableView() 2910 table_view.setModel(csv_model) 2911 2912 tmp_protein_pair = self._current_project.search_protein_pair( 2913 self._view.ui.cb_results_analysis_options.currentText(), 2914 ) 2915 csv_filepath = pathlib.Path(f"{constants.CACHE_CSV_DIR}/{tmp_protein_pair.name}.csv") 2916 if not os.path.exists(constants.CACHE_CSV_DIR): 2917 os.mkdir(constants.CACHE_CSV_DIR) 2918 tmp_protein_pair = self._current_project.search_protein_pair(self.results_name) 2919 2920 distance_data = tmp_protein_pair.distance_analysis.analysis_results.distance_data 2921 distance_data_array = np.array( 2922 [ 2923 distance_data[pyssa_keys.ARRAY_DISTANCE_INDEX], 2924 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_1_CHAIN], 2925 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_1_POSITION], 2926 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_1_RESI], 2927 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_2_CHAIN], 2928 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_2_POSITION], 2929 distance_data[pyssa_keys.ARRAY_DISTANCE_PROT_2_RESI], 2930 distance_data[pyssa_keys.ARRAY_DISTANCE_DISTANCES], 2931 ], 2932 ) 2933 distance_data_array_transpose = distance_data_array.transpose() 2934 with open(csv_filepath, mode="w", newline="") as file: 2935 writer = csv.writer(file, delimiter=",") 2936 writer.writerows(distance_data_array_transpose) 2937 2938 file.close() 2939 2940 with open(csv_filepath, "r", encoding="utf-8") as csv_file: 2941 i = 0 2942 for line in csv_file: 2943 tmp_list = line.split(",") 2944 # tmp_list.pop(0) 2945 standard_item_list = [] 2946 pair_no_item = QtGui.QStandardItem() 2947 pair_no_item.setData(int(tmp_list[0]), role=QtCore.Qt.DisplayRole) 2948 ref_chain_item = QtGui.QStandardItem() 2949 ref_chain_item.setData(str(tmp_list[1]), role=QtCore.Qt.DisplayRole) 2950 ref_pos_item = QtGui.QStandardItem() 2951 ref_pos_item.setData(int(tmp_list[2]), role=QtCore.Qt.DisplayRole) 2952 ref_resi_item = QtGui.QStandardItem() 2953 ref_resi_item.setData(str(tmp_list[3]), role=QtCore.Qt.DisplayRole) 2954 model_chain_item = QtGui.QStandardItem() 2955 model_chain_item.setData(str(tmp_list[4]), role=QtCore.Qt.DisplayRole) 2956 model_pos_item = QtGui.QStandardItem() 2957 model_pos_item.setData(int(tmp_list[5]), role=QtCore.Qt.DisplayRole) 2958 model_resi_item = QtGui.QStandardItem() 2959 model_resi_item.setData(str(tmp_list[6]), role=QtCore.Qt.DisplayRole) 2960 distance_item = QtGui.QStandardItem() 2961 distance_item.setData(float(tmp_list[7]), role=QtCore.Qt.DisplayRole) 2962 standard_item_list.append(pair_no_item) 2963 standard_item_list.append(ref_chain_item) 2964 standard_item_list.append(ref_pos_item) 2965 standard_item_list.append(ref_resi_item) 2966 standard_item_list.append(model_chain_item) 2967 standard_item_list.append(model_pos_item) 2968 standard_item_list.append(model_resi_item) 2969 standard_item_list.append(distance_item) 2970 csv_model.insertRow(i, standard_item_list) 2971 i += 1 2972 csv_file.close() 2973 csv_model.removeRow(0) 2974 table_view.setAlternatingRowColors(True) 2975 table_view.resizeColumnsToContents() 2976 table_view.verticalHeader().setVisible(False) 2977 table_view.setSortingEnabled(True) 2978 table_view.sortByColumn(0, QtCore.Qt.AscendingOrder) 2979 table_dialog_layout = QtWidgets.QHBoxLayout() 2980 table_dialog_layout.addWidget(table_view) 2981 table_dialog.setLayout(table_dialog_layout) 2982 # styles 2983 stylesheet = """ 2984 QDialog {background-color: #F6F4F8;} 2985 QTableView {background-color: white;} 2986 """ 2987 table_dialog.setStyleSheet(stylesheet) 2988 table_dialog.setWindowFlag(QtCore.Qt.WindowMaximizeButtonHint, True) 2989 table_dialog.setWindowFlag(QtCore.Qt.WindowCloseButtonHint, True) 2990 table_dialog.setModal(True) 2991 table_view.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers) # disables editing of cells 2992 table_dialog.setWindowTitle("Distances of Structure Alignment") 2993 table_dialog.show()
Displays the distances in a table.
def
choose_manage_open_protein(self) -> None:
2998 def choose_manage_open_protein(self) -> None: 2999 """Shows the different configuration gui elements.""" 3000 if self._view.ui.box_manage_choose_protein.currentText() != "": 3001 gui_elements_to_show = [ 3002 self._view.ui.lbl_manage_choose_color, 3003 self._view.ui.box_manage_choose_color, 3004 self._view.ui.lbl_manage_choose_representation, 3005 self._view.ui.box_manage_choose_representation, 3006 self._view.ui.lbl_manage_choose_bg_color, 3007 self._view.ui.box_manage_choose_bg_color, 3008 ] 3009 gui_utils.show_gui_elements(gui_elements_to_show) 3010 tmp_pymol_selection_option: str = "byres (resn CYS and name SG) within 2 of (resn CYS and name SG)" 3011 if ( 3012 cmd.select( 3013 name="disulfides", 3014 selection=f"{self._view.ui.box_manage_choose_protein.currentText()} & {tmp_pymol_selection_option}", 3015 ) 3016 > 0 3017 ): 3018 gui_elements_to_show = [ 3019 self._view.ui.lbl_disulfid_bond_1, 3020 self._view.ui.lbl_disulfid_bond_2, 3021 self._view.ui.btn_disulfid_bond_show, 3022 self._view.ui.btn_disulfid_bond_hide, 3023 ] 3024 gui_utils.show_gui_elements(gui_elements_to_show) 3025 else: 3026 gui_elements_to_hide = [ 3027 self._view.ui.lbl_manage_choose_color, 3028 self._view.ui.box_manage_choose_color, 3029 self._view.ui.lbl_manage_choose_representation, 3030 self._view.ui.box_manage_choose_representation, 3031 self._view.ui.lbl_manage_choose_bg_color, 3032 self._view.ui.box_manage_choose_bg_color, 3033 self._view.ui.lbl_disulfid_bond_1, 3034 self._view.ui.lbl_disulfid_bond_2, 3035 self._view.ui.btn_disulfid_bond_show, 3036 self._view.ui.btn_disulfid_bond_hide, 3037 ] 3038 gui_utils.hide_gui_elements(gui_elements_to_hide)
Shows the different configuration gui elements.
def
choose_manage_color_selected_protein(self) -> None:
3040 def choose_manage_color_selected_protein(self) -> None: 3041 """Sets the protein color.""" 3042 tmp_input = self._view.ui.box_manage_choose_protein.currentText() 3043 tmp_protein = self._current_project.search_protein(tmp_input) 3044 tmp_protein.color_protein_in_pymol( 3045 self._view.ui.box_manage_choose_color.currentText(), 3046 f"/{tmp_protein.get_molecule_object()}", 3047 )
Sets the protein color.
def
choose_manage_representation(self) -> None:
3049 def choose_manage_representation(self) -> None: 3050 """Sets the representation.""" 3051 tmp_input = self._view.ui.box_manage_choose_protein.currentText() 3052 tmp_protein = self._current_project.search_protein(tmp_input) 3053 tmp_selection = f"/{tmp_protein.get_molecule_object()}" 3054 if self._view.ui.box_manage_choose_representation.currentIndex() == 0: 3055 print("Please select a representation.") 3056 self._view.status_bar.showMessage("Please select a representation.") 3057 elif self._view.ui.box_manage_choose_representation.currentIndex() == 1: 3058 cmd.show("cartoon", tmp_selection) 3059 cmd.hide("ribbon", tmp_selection) 3060 elif self._view.ui.box_manage_choose_representation.currentIndex() == 2: 3061 cmd.show("ribbon", tmp_selection) 3062 cmd.hide("cartoon", tmp_selection) 3063 else: 3064 print("Missing implementation!")
Sets the representation.
def
choose_manage_bg_color(self) -> None:
3066 def choose_manage_bg_color(self) -> None: 3067 """Sets the background color.""" 3068 if self._view.ui.box_manage_choose_bg_color.currentIndex() == 0: 3069 print("Please select a background color.") 3070 self._view.status_bar.showMessage("Please select a background color.") 3071 elif self._view.ui.box_manage_choose_bg_color.currentIndex() == 1: 3072 cmd.bg_color("black") 3073 elif self._view.ui.box_manage_choose_bg_color.currentIndex() == 2: 3074 cmd.bg_color("white") 3075 else: 3076 print("Missing implementation!")
Sets the background color.
def
show_disulfid_bonds_as_sticks(self) -> None:
3078 def show_disulfid_bonds_as_sticks(self) -> None: 3079 """Shows all disulfid bonds within the pymol session.""" 3080 tmp_pymol_selection_option: str = "byres (resn CYS and name SG) within 2 of (resn CYS and name SG)" 3081 cmd.select( 3082 name="disulfides", 3083 selection=f"{self._view.ui.box_manage_choose_protein.currentText()} & {tmp_pymol_selection_option}", 3084 ) 3085 cmd.color(color="atomic", selection="disulfides and not elem C") 3086 cmd.set("valence", 0) # this needs to be better implemented 3087 cmd.show("sticks", "disulfides") 3088 cmd.hide("sticks", "elem H")
Shows all disulfid bonds within the pymol session.
def
hide_disulfid_bonds_as_sticks(self) -> None:
3090 def hide_disulfid_bonds_as_sticks(self) -> None: 3091 """Hides all disulfid bonds within the pymol session.""" 3092 tmp_pymol_selection_option: str = "byres (resn CYS and name SG) within 2 of (resn CYS and name SG)" 3093 cmd.select( 3094 name="disulfides", 3095 selection=f"{self._view.ui.box_manage_choose_protein.currentText()} & {tmp_pymol_selection_option}", 3096 ) 3097 cmd.hide("sticks", "disulfides")
Hides all disulfid bonds within the pymol session.
def
show_representation(self) -> None:
3102 def show_representation(self) -> None: 3103 """Sets the representation.""" 3104 if self._view.ui.box_representation.currentIndex() == 0: 3105 self.main_window_state.image_page.representation = "" 3106 self._view.status_bar.showMessage("Please select a representation.") 3107 elif self._view.ui.box_representation.currentIndex() == 1: 3108 cmd.show("cartoon", "all") 3109 cmd.hide("ribbon", "all") 3110 self.main_window_state.image_page.representation = "cartoon" 3111 elif self._view.ui.box_representation.currentIndex() == 2: 3112 cmd.show("ribbon", "all") 3113 cmd.hide("cartoon", "all") 3114 self.main_window_state.image_page.representation = "ribbon" 3115 else: 3116 print("Missing implementation!")
Sets the representation.
def
choose_bg_color(self) -> None:
3118 def choose_bg_color(self) -> None: 3119 """Sets the background color.""" 3120 if self._view.ui.box_bg_color.currentIndex() == 0: 3121 self.main_window_state.image_page.background_color = "" 3122 self._view.status_bar.showMessage("Please select a background color.") 3123 elif self._view.ui.box_bg_color.currentIndex() == 1: 3124 cmd.bg_color("black") 3125 self.main_window_state.image_page.background_color = "black" 3126 elif self._view.ui.box_bg_color.currentIndex() == 2: 3127 cmd.bg_color("white") 3128 self.main_window_state.image_page.background_color = "white" 3129 else: 3130 print("Missing implementation!")
Sets the background color.
def
choose_renderer(self) -> None:
3132 def choose_renderer(self) -> None: 3133 """Sets the renderer.""" 3134 if self._view.ui.box_renderer.currentIndex() == 0: 3135 self._view.status_bar.showMessage("Please select a renderer.") 3136 self._view.ui.cb_ray_tracing.hide() 3137 self._view.ui.label_26.hide() 3138 elif self._view.ui.box_renderer.currentIndex() == 1: 3139 self.renderer = "-1" 3140 self._view.ui.cb_ray_tracing.show() 3141 self._view.ui.label_26.show() 3142 elif self._view.ui.box_renderer.currentIndex() == 2: 3143 self.renderer = "0" 3144 self._view.ui.cb_ray_tracing.show() 3145 self._view.ui.label_26.show() 3146 else: 3147 print("Missing implementation!") 3148 self.main_window_state.image_page.renderer = self._view.ui.box_renderer.currentIndex()
Sets the renderer.
def
choose_ray_trace_mode(self) -> None:
3150 def choose_ray_trace_mode(self) -> None: 3151 """Sets the ray-trace mode.""" 3152 if self._view.ui.box_ray_trace_mode.currentIndex() == 0: 3153 self._view.status_bar.showMessage("Please select a Ray-Trace-Mode.") 3154 elif self._view.ui.box_ray_trace_mode.currentIndex() == 1: 3155 cmd.set("ray_trace_mode", 0) 3156 elif self._view.ui.box_ray_trace_mode.currentIndex() == 2: 3157 cmd.set("ray_trace_mode", 1) 3158 elif self._view.ui.box_ray_trace_mode.currentIndex() == 3: 3159 cmd.set("ray_trace_mode", 2) 3160 elif self._view.ui.box_ray_trace_mode.currentIndex() == 4: 3161 cmd.set("ray_trace_mode", 3) 3162 else: 3163 print("Missing implementation!") 3164 self.main_window_state.image_page.ray_trace_mode = self._view.ui.box_ray_trace_mode.currentIndex()
Sets the ray-trace mode.
def
choose_ray_texture(self) -> None:
3166 def choose_ray_texture(self) -> None: 3167 """Sets the ray texture.""" 3168 if self._view.ui.box_ray_texture.currentIndex() == 0: 3169 print("Please select a Ray Texture.") 3170 self._view.status_bar.showMessage("Please select a Ray Texture.") 3171 elif self._view.ui.box_ray_texture.currentIndex() == 1: 3172 cmd.set("ray_texture", 0) 3173 elif self._view.ui.box_ray_texture.currentIndex() == 2: 3174 cmd.set("ray_texture", 1) 3175 elif self._view.ui.box_ray_texture.currentIndex() == 3: 3176 cmd.set("ray_texture", 2) 3177 elif self._view.ui.box_ray_texture.currentIndex() == 4: 3178 cmd.set("ray_texture", 3) 3179 elif self._view.ui.box_ray_texture.currentIndex() == 5: 3180 cmd.set("ray_texture", 4) 3181 elif self._view.ui.box_ray_texture.currentIndex() == 6: 3182 cmd.set("ray_texture", 5) 3183 else: 3184 print("Missing implementation!") 3185 self.main_window_state.image_page.ray_texture = self._view.ui.box_ray_texture.currentIndex()
Sets the ray texture.
def
decide_ray_tracing(self) -> None:
3187 def decide_ray_tracing(self) -> None: 3188 """Sets the ray-tracing options.""" 3189 print(self._view.ui.cb_ray_tracing.isChecked()) 3190 if self._view.ui.cb_ray_tracing.isChecked(): 3191 self._view.ui.cb_transparent_bg.hide() 3192 self._view.ui.label_23.hide() 3193 self._view.ui.box_renderer.setEnabled(False) 3194 self._view.ui.label_10.show() 3195 self._view.ui.box_ray_trace_mode.show() 3196 self._view.ui.label_14.show() 3197 self._view.ui.box_ray_texture.show() 3198 cmd.set("ray_opaque_background", "off") 3199 else: 3200 self._view.ui.cb_transparent_bg.show() 3201 self._view.ui.label_23.show() 3202 self._view.ui.box_renderer.setEnabled(True) 3203 self._view.ui.label_10.hide() 3204 self._view.ui.box_ray_trace_mode.hide() 3205 self._view.ui.label_14.hide() 3206 self._view.ui.box_ray_texture.hide() 3207 self.main_window_state.image_page.ray_tracing = self._view.ui.cb_ray_tracing.isChecked()
Sets the ray-tracing options.
def
decide_transparent_bg(self) -> None:
3209 def decide_transparent_bg(self) -> None: 3210 """Sets the transparent background.""" 3211 if self._view.ui.cb_transparent_bg.isChecked(): 3212 cmd.set("opaque_background", "off") 3213 else: 3214 cmd.set("opaque_background", "on") 3215 self.main_window_state.image_page.transparent_background = self._view.ui.cb_transparent_bg.isChecked()
Sets the transparent background.
@staticmethod
def
update_scene() -> None:
3217 @staticmethod 3218 def update_scene() -> None: 3219 """Updates the current selected PyMOL scene.""" 3220 cmd.scene(key="auto", action="update")
Updates the current selected PyMOL scene.
def
save_scene(self) -> None:
3222 def save_scene(self) -> None: 3223 """Saves the current view as a new PyMOL scene.""" 3224 # returns tuple with (name, bool) 3225 scene_name = QtWidgets.QInputDialog.getText(self._view, "Save Scene", "Enter scene name:") 3226 if scene_name[1]: 3227 cmd.scene(key=scene_name[0], action="append")
Saves the current view as a new PyMOL scene.
def
post_preview_image(self) -> None:
3229 def post_preview_image(self) -> None: 3230 """Hides the block box of the preview process.""" 3231 self.block_box_uni.hide() 3232 self.block_box_uni.destroy(True) 3233 self._view.status_bar.showMessage("Finished preview of ray-traced image.") 3234 QtWidgets.QApplication.restoreOverrideCursor()
Hides the block box of the preview process.
def
preview_image(self) -> None:
3236 def preview_image(self) -> None: 3237 """Previews the image.""" 3238 QtWidgets.QApplication.setOverrideCursor(Qt.WaitCursor) 3239 if self._view.ui.cb_ray_tracing.isChecked(): 3240 self._view.status_bar.showMessage("Preview ray-traced image ...") 3241 # <editor-fold desc="Worker setup"> 3242 # --Begin: worker setup 3243 self.tmp_thread = QtCore.QThread() 3244 self.tmp_worker = task_workers.PreviewRayImageWorker(self.renderer) 3245 self.tmp_thread = task_workers.setup_worker_for_work( 3246 self.tmp_thread, 3247 self.tmp_worker, 3248 self.display_view_page, 3249 ) 3250 self.tmp_worker.finished.connect(self.post_preview_image) 3251 self.tmp_thread.start() 3252 # --End: worker setup 3253 3254 # </editor-fold> 3255 gui_utils.setup_standard_block_box( 3256 self.block_box_uni, 3257 "Preview ray-trace image", 3258 "Creating preview for the ray-traced image ...", 3259 ) 3260 self.block_box_uni.exec_() 3261 else: 3262 self._view.status_bar.showMessage("Preview draw image ...") 3263 cmd.draw(2400, 2400) 3264 self._view.status_bar.showMessage("Finished preview of drawn image.") 3265 QtWidgets.QApplication.restoreOverrideCursor()
Previews the image.
def
post_save_image(self) -> None:
3267 def post_save_image(self) -> None: 3268 """Displays a message box which informs that the process has finished.""" 3269 self.block_box_uni.hide() 3270 self.block_box_uni.destroy(True) 3271 self._view.status_bar.showMessage("Finished image creation.") 3272 QtWidgets.QApplication.restoreOverrideCursor() 3273 basic_boxes.ok("Finished image creation", "The image has been created.", QtWidgets.QMessageBox.Information)
Displays a message box which informs that the process has finished.
def
save_image(self) -> None:
3275 def save_image(self) -> None: 3276 """Saves the image as a png file.""" 3277 QtWidgets.QApplication.setOverrideCursor(Qt.WaitCursor) 3278 if self._view.ui.cb_ray_tracing.isChecked(): 3279 save_dialog = QtWidgets.QFileDialog() 3280 try: 3281 full_file_name = save_dialog.getSaveFileName(caption="Save Image", filter="Image (*.png)") 3282 if full_file_name == ("", ""): 3283 tools.quick_log_and_display( 3284 "info", 3285 "No file has been selected.", 3286 self._view.status_bar, 3287 "No file has been selected.", 3288 ) 3289 return 3290 self._view.status_bar.showMessage("Creating ray-traced image ...") 3291 3292 # <editor-fold desc="Worker setup"> 3293 # --Begin: worker setup 3294 self.tmp_thread = QtCore.QThread() 3295 self.tmp_worker = task_workers.SaveRayImageWorker(self.renderer, full_file_name[0]) 3296 self.tmp_thread = task_workers.setup_worker_for_work( 3297 self.tmp_thread, 3298 self.tmp_worker, 3299 self.display_view_page, 3300 ) 3301 self.tmp_worker.finished.connect(self.post_save_image) 3302 self.tmp_thread.start() 3303 # --End: worker setup 3304 3305 # </editor-fold> 3306 gui_utils.setup_standard_block_box( 3307 self.block_box_uni, 3308 "Save ray-trace image", 3309 "Creating the ray-traced image ...", 3310 ) 3311 self.block_box_uni.exec_() 3312 3313 # cmd.ray(2400, 2400, renderer=int(self.renderer)) 3314 # cmd.png(full_file_name[0], dpi=300) 3315 3316 except FileExistsError: 3317 tools.quick_log_and_display( 3318 "error", 3319 "File exists already.", 3320 self._view.status_bar, 3321 "File exists already.", 3322 ) 3323 except pymol.CmdException: 3324 tools.quick_log_and_display( 3325 "error", 3326 "Unexpected Error from PyMOL while saving the " "an image", 3327 self._view.status_bar, 3328 "Unexpected Error from PyMOL", 3329 ) 3330 else: 3331 save_dialog = QtWidgets.QFileDialog() 3332 try: 3333 full_file_name = save_dialog.getSaveFileName(caption="Save Image", filter="Image (*.png)") 3334 if full_file_name == ("", ""): 3335 tools.quick_log_and_display( 3336 "info", 3337 "No file has been selected.", 3338 self._view.status_bar, 3339 "No file has been selected.", 3340 ) 3341 return 3342 self._view.status_bar.showMessage("Creating draw image ...") 3343 cmd.draw(2400, 2400) 3344 cmd.png(full_file_name[0], dpi=300) 3345 self._view.status_bar.showMessage("Finished image creation.") 3346 basic_boxes.ok( 3347 "Finished image creation", 3348 "The image has been created.", 3349 QtWidgets.QMessageBox.Information, 3350 ) 3351 except FileExistsError: 3352 tools.quick_log_and_display( 3353 "error", 3354 "File exists already.", 3355 self._view.status_bar, 3356 "File exists already.", 3357 ) 3358 except pymol.CmdException: 3359 tools.quick_log_and_display( 3360 "error", 3361 "Unexpected Error from PyMOL while saving the " "an image", 3362 self._view.status_bar, 3363 "Unexpected Error from PyMOL", 3364 ) 3365 finally: 3366 QtWidgets.QApplication.restoreOverrideCursor()
Saves the image as a png file.
def
open_protein_for_hotspots(self) -> None:
3371 def open_protein_for_hotspots(self) -> None: 3372 """Loads the selected protein's pymol session.""" 3373 self._view.wait_spinner.start() 3374 try: 3375 tmp_name = self._view.ui.list_hotspots_choose_protein.currentItem().text() 3376 except AttributeError: 3377 self._view.wait_spinner.stop() 3378 return 3379 if self._view.ui.list_hotspots_choose_protein.currentItem().text() != "": 3380 tools.ask_to_save_pymol_session(self._current_project, self.current_session, self._application_settings) 3381 self._active_task = tasks.Task( 3382 target=main_presenter_async.open_protein_for_hotspots, 3383 args=( 3384 tmp_name, 3385 self._current_project, 3386 self.current_session, 3387 ), 3388 post_func=self.__await_open_protein_for_hotspots, 3389 ) 3390 self._active_task.start() 3391 self.update_status("Loading PyMOL session ...") 3392 else: 3393 self._view.wait_spinner.stop() 3394 self.update_status(self._workspace_status)
Loads the selected protein's pymol session.
@staticmethod
def
hide_resi_sticks() -> None:
3425 @staticmethod 3426 def hide_resi_sticks() -> None: 3427 """Hides the balls and sticks representation of the pymol selection.""" 3428 session_util.check_if_sele_is_empty() 3429 cmd.hide(representation="sticks", selection="sele")
Hides the balls and sticks representation of the pymol selection.
@staticmethod
def
show_resi_sticks() -> None:
3431 @staticmethod 3432 def show_resi_sticks() -> None: 3433 """Shows the pymol selection as sticks.""" 3434 session_util.check_if_sele_is_empty() 3435 cmd.show(representation="sticks", selection="sele and not hydrogens") 3436 cmd.select(name="sele", selection="sele and not hydrogens") 3437 cmd.color(color="atomic", selection="sele and not elem C") 3438 cmd.set("valence", 0) # this needs to be better implemented
Shows the pymol selection as sticks.
@staticmethod
def
zoom_resi_position() -> None:
3440 @staticmethod 3441 def zoom_resi_position() -> None: 3442 """Zooms to the pymol selection.""" 3443 session_util.check_if_sele_is_empty() 3444 cmd.zoom(selection="sele", buffer=8.0, state=0, complete=0)
Zooms to the pymol selection.
def
display_home_page(self) -> None:
3746 def display_home_page(self) -> None: 3747 """Displays the homepage of the plugin.""" 3748 if self.is_distance_plot_open: 3749 self.distance_plot_dialog.close() 3750 self.is_distance_plot_open = False 3751 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 0, "Home")
Displays the homepage of the plugin.
def
display_job_analysis_page(self) -> None:
3753 def display_job_analysis_page(self) -> None: 3754 """Displays the job analysis work area.""" 3755 self._view.ui.list_analysis_batch_ref_chains.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection) 3756 self._view.ui.list_analysis_batch_model_chains.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection) 3757 # regular work area opening 3758 self._init_batch_analysis_page() 3759 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 4, "Structure Analysis") 3760 self.last_sidebar_button = styles.color_sidebar_buttons( 3761 self.last_sidebar_button, 3762 self._view.ui.btn_batch_analysis_page, 3763 )
Displays the job analysis work area.
def
display_results_page(self) -> None:
3765 def display_results_page(self) -> None: 3766 """Displays the results work area.""" 3767 if self.is_distance_plot_open: 3768 self.distance_plot_dialog.close() 3769 self.is_distance_plot_open = False 3770 results = [] 3771 results.insert(0, "") 3772 3773 for tmp_protein_pair in self._current_project.protein_pairs: 3774 results.append(tmp_protein_pair.name) 3775 if tmp_protein_pair.name == self.results_name: 3776 pass 3777 self._view.ui.cb_results_analysis_options.clear() 3778 gui_utils.fill_combo_box(self._view.ui.cb_results_analysis_options, results) 3779 3780 desired_string: str = self.main_window_state.results_page.results_name 3781 # Find the index of the string in the combo box 3782 index = self._view.ui.cb_results_analysis_options.findText(desired_string) 3783 # Set the current index of the combo box 3784 if index != -1: 3785 self._view.ui.cb_results_analysis_options.setCurrentIndex(index) 3786 else: 3787 print(f"String '{desired_string}' not found in the combo box.") 3788 3789 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 5, "Results") 3790 self.last_sidebar_button = styles.color_sidebar_buttons( 3791 self.last_sidebar_button, 3792 self._view.ui.btn_results_page, 3793 )
Displays the results work area.
def
display_image_page(self) -> None:
3795 def display_image_page(self) -> None: 3796 """Displays the image work area.""" 3797 if self.is_distance_plot_open: 3798 self.distance_plot_dialog.close() 3799 self.is_distance_plot_open = False 3800 self._init_image_page() 3801 3802 if self.main_window_state.image_page.transparent_background: 3803 self._view.ui.cb_transparent_bg.setChecked(True) 3804 else: 3805 self._view.ui.cb_transparent_bg.setChecked(False) 3806 if self.main_window_state.image_page.ray_tracing: 3807 self._view.ui.cb_ray_tracing.setChecked(True) 3808 else: 3809 self._view.ui.cb_ray_tracing.setChecked(False) 3810 try: 3811 self._view.ui.box_representation.setCurrentIndex( 3812 self._view.ui.box_representation.findText(self.main_window_state.image_page.representation), 3813 ) 3814 self._view.ui.box_bg_color.setCurrentIndex( 3815 self._view.ui.box_bg_color.findText(self.main_window_state.image_page.background_color), 3816 ) 3817 self._view.ui.box_renderer.setCurrentIndex(self.main_window_state.image_page.renderer) 3818 self._view.ui.box_ray_trace_mode.setCurrentIndex(self.main_window_state.image_page.ray_trace_mode) 3819 self._view.ui.box_ray_texture.setCurrentIndex(self.main_window_state.image_page.ray_texture) 3820 except IndexError: 3821 constants.PYSSA_LOGGER.error("An option is invalid.") 3822 3823 if self._view.ui.box_renderer.currentText() == "": 3824 self._view.ui.cb_ray_tracing.hide() 3825 self._view.ui.label_26.hide() 3826 else: 3827 self._view.ui.cb_ray_tracing.show() 3828 self._view.ui.label_26.show() 3829 3830 if self._view.ui.cb_ray_tracing.isChecked(): 3831 self._view.ui.label_10.show() 3832 self._view.ui.box_ray_trace_mode.show() 3833 self._view.ui.label_14.show() 3834 self._view.ui.box_ray_texture.show() 3835 else: 3836 self._view.ui.label_10.hide() 3837 self._view.ui.box_ray_trace_mode.hide() 3838 self._view.ui.label_14.hide() 3839 self._view.ui.box_ray_texture.hide() 3840 3841 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_image_page) 3842 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 6, "Image")
Displays the image work area.
def
display_new_page(self) -> None:
3844 def display_new_page(self) -> None: 3845 """Displays the new project work area.""" 3846 self._init_new_page() 3847 self._view.ui.list_new_projects.clear() 3848 # pre-process 3849 gui_elements_to_hide = [ 3850 self._view.ui.lbl_new_choose_reference, 3851 self._view.ui.txt_new_choose_reference, 3852 self._view.ui.btn_new_choose_reference, 3853 ] 3854 gui_utils.hide_gui_elements(gui_elements_to_hide) 3855 self._view.status_bar.showMessage(self._workspace_label.text()) 3856 tools.scan_workspace_for_valid_projects(self._workspace_path, self._view.ui.list_new_projects) 3857 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 7, "Create new project") 3858 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_new_page)
Displays the new project work area.
def
display_open_page(self) -> None:
3860 def display_open_page(self) -> None: 3861 """Displays the open project work area.""" 3862 self._view.ui.txt_open_search.clear() 3863 self._view.ui.txt_open_selected_project.clear() 3864 if safeguard.Safeguard.check_filepath(self._workspace_path): 3865 self._view.ui.list_open_projects.clear() 3866 # pre-process 3867 self._view.status_bar.showMessage(self._workspace_label.text()) 3868 try: 3869 tools.scan_workspace_for_valid_projects(self._workspace_path, self._view.ui.list_open_projects) 3870 except PermissionError: 3871 gui_utils.error_dialog_settings( 3872 "The settings file is corrupted. Please restore the settings!", 3873 "", 3874 self._application_settings, 3875 ) 3876 self.display_home_page() 3877 return 3878 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 8, "Open existing project") 3879 self.last_sidebar_button = styles.color_sidebar_buttons( 3880 self.last_sidebar_button, 3881 self._view.ui.btn_open_page, 3882 ) 3883 else: 3884 gui_utils.error_dialog_settings( 3885 "The settings file is corrupted. Please restore the settings!", 3886 "", 3887 self._application_settings, 3888 ) 3889 self.display_home_page()
Displays the open project work area.
def
display_delete_page(self) -> None:
3891 def display_delete_page(self) -> None: 3892 """Displays the "delete" project work area.""" 3893 self._view.ui.txt_delete_search.clear() 3894 self._view.ui.txt_delete_selected_projects.clear() 3895 self._view.ui.list_delete_projects.clear() 3896 # pre-process 3897 self._view.status_bar.showMessage(self._workspace_label.text()) 3898 tools.scan_workspace_for_valid_projects(self._workspace_path, self._view.ui.list_delete_projects) 3899 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 9, "Delete existing project") 3900 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_delete_page)
Displays the "delete" project work area.
def
display_edit_page(self) -> None:
3902 def display_edit_page(self) -> None: 3903 """Displays the edit project page.""" 3904 if self.is_distance_plot_open: 3905 self.distance_plot_dialog.close() 3906 self.is_distance_plot_open = False 3907 # pre-process 3908 self._view.status_bar.showMessage(self._workspace_label.text()) 3909 self._init_edit_page() 3910 tools.switch_page( 3911 self._view.ui.stackedWidget, 3912 self._view.ui.lbl_page_title, 3913 13, 3914 "Edit proteins of current project", 3915 ) 3916 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_edit_page) 3917 if len(self._view.ui.list_edit_project_proteins) >= 2: 3918 self._view.ui.btn_edit_existing_protein_struct.hide() 3919 self._view.ui.lbl_edit_existing_protein_struct.hide() 3920 else: 3921 self._view.ui.btn_edit_existing_protein_struct.show() 3922 self._view.ui.lbl_edit_existing_protein_struct.show()
Displays the edit project page.
def
display_hotspots_page(self) -> None:
3924 def display_hotspots_page(self) -> None: 3925 """Displays the hotspots page.""" 3926 if self.is_distance_plot_open: 3927 self.distance_plot_dialog.close() 3928 self.is_distance_plot_open = False 3929 try: 3930 print(self._view.ui.list_hotspots_choose_protein.currentItem().text()) 3931 except AttributeError: 3932 self._view.ui.list_hotspots_choose_protein.clear() 3933 gui_elements_to_hide = [ 3934 self._view.ui.lbl_hotspots_resi_no, 3935 self._view.ui.sp_hotspots_resi_no, 3936 self._view.ui.lbl_hotspots_resi_show, 3937 self._view.ui.btn_hotspots_resi_show, 3938 self._view.ui.lbl_hotspots_resi_hide, 3939 self._view.ui.btn_hotspots_resi_hide, 3940 self._view.ui.lbl_hotspots_resi_zoom, 3941 self._view.ui.btn_hotspots_resi_zoom, 3942 ] 3943 gui_utils.hide_gui_elements(gui_elements_to_hide) 3944 gui_utils.fill_list_view_with_protein_names( 3945 self._current_project, 3946 self._view.ui.list_hotspots_choose_protein, 3947 ) 3948 gui_utils.fill_list_view_with_protein_pair_names( 3949 self._current_project, 3950 self._view.ui.list_hotspots_choose_protein, 3951 ) 3952 # self.project_scanner.scan_project_for_valid_proteins(self._view.ui.list_hotspots_choose_protein) 3953 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 18, "Hotspots") 3954 self.last_sidebar_button = styles.color_sidebar_buttons( 3955 self.last_sidebar_button, 3956 self._view.ui.btn_hotspots_page, 3957 )
Displays the hotspots page.
def
display_manage_pymol_session(self) -> None:
3959 def display_manage_pymol_session(self) -> None: 3960 """Displays the manage pymol session page.""" 3961 if self.is_distance_plot_open: 3962 self.distance_plot_dialog.close() 3963 self.is_distance_plot_open = False 3964 self._view.ui.box_manage_choose_protein.clear() 3965 pymol_objs = cmd.get_object_list() 3966 pymol_objs.insert(0, "") 3967 for tmp_object in pymol_objs: 3968 self._view.ui.box_manage_choose_protein.addItem(tmp_object) 3969 self._view.ui.box_manage_choose_protein.setCurrentIndex( 3970 self.pymol_session_specs[pyssa_keys.SESSION_SPEC_PROTEIN][0], 3971 ) 3972 self._view.ui.box_manage_choose_color.setCurrentIndex( 3973 self.pymol_session_specs[pyssa_keys.SESSION_SPEC_COLOR][0], 3974 ) 3975 self._view.ui.box_manage_choose_representation.setCurrentIndex( 3976 self.pymol_session_specs[pyssa_keys.SESSION_SPEC_REPRESENTATION][0], 3977 ) 3978 self._view.ui.box_manage_choose_bg_color.setCurrentIndex( 3979 self.pymol_session_specs[pyssa_keys.SESSION_SPEC_BG_COLOR][0], 3980 ) 3981 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 24, "Manage PyMOL session") 3982 self.last_sidebar_button = styles.color_sidebar_buttons( 3983 self.last_sidebar_button, 3984 self._view.ui.btn_manage_session, 3985 ) 3986 gui_elements_to_hide = [ 3987 self._view.ui.lbl_manage_choose_color, 3988 self._view.ui.box_manage_choose_color, 3989 self._view.ui.lbl_manage_choose_representation, 3990 self._view.ui.box_manage_choose_representation, 3991 self._view.ui.lbl_manage_choose_bg_color, 3992 self._view.ui.box_manage_choose_bg_color, 3993 self._view.ui.lbl_disulfid_bond_1, 3994 self._view.ui.lbl_disulfid_bond_2, 3995 self._view.ui.btn_disulfid_bond_show, 3996 self._view.ui.btn_disulfid_bond_hide, 3997 ] 3998 gui_utils.hide_gui_elements(gui_elements_to_hide)
Displays the manage pymol session page.
def
show_add_reference(self) -> None:
4003 def show_add_reference(self) -> None: 4004 """Shows the reference input section.""" 4005 # checkbox is checked 4006 self._view.ui.cb_new_add_reference.checkState() 4007 if self._view.ui.cb_new_add_reference.checkState() == 2: 4008 self._view.ui.txt_new_choose_reference.clear() 4009 self._view.ui.txt_new_choose_reference.setStyleSheet("background-color: white") 4010 self._view.ui.lbl_new_choose_reference.show() 4011 self._view.ui.txt_new_choose_reference.show() 4012 self._view.ui.btn_new_choose_reference.show() 4013 self._view.ui.btn_new_create_project.setEnabled(False) 4014 styles.color_button_not_ready(self._view.ui.btn_new_create_project) 4015 # check internet connectivity 4016 if not tools.check_internet_connectivity(): 4017 gui_utils.no_internet_dialog() 4018 self._view.ui.txt_new_choose_reference.setEnabled(False) 4019 self._view.ui.lbl_new_status_choose_reference.setText("You cannot enter a PDB ID (no internet).") 4020 return 4021 self._view.ui.txt_new_choose_reference.setEnabled(True) 4022 self._view.ui.lbl_new_status_choose_reference.setText("") 4023 else: 4024 self._view.ui.lbl_new_choose_reference.hide() 4025 self._view.ui.txt_new_choose_reference.hide() 4026 self._view.ui.btn_new_choose_reference.hide() 4027 self._view.ui.lbl_new_status_choose_reference.setText("") 4028 self._view.ui.btn_new_create_project.setEnabled(True)
Shows the reference input section.
def
load_reference_in_project(self) -> None:
4030 def load_reference_in_project(self) -> None: 4031 """Loads a reference in a new project.""" 4032 try: 4033 # open file dialog 4034 file_name = QtWidgets.QFileDialog.getOpenFileName( 4035 self._view, 4036 "Open Reference", 4037 QtCore.QDir.homePath(), 4038 "PDB Files (*.pdb)", 4039 ) 4040 if file_name == ("", ""): 4041 raise ValueError 4042 # display path in text box 4043 self._view.ui.txt_new_choose_reference.setText(str(file_name[0])) 4044 self._view.ui.txt_new_choose_reference.setEnabled(False) 4045 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #000000") 4046 self._view.ui.btn_new_create_project.setEnabled(True) 4047 except ValueError: 4048 print("No file has been selected.")
Loads a reference in a new project.
def
validate_reference_in_project(self) -> None:
4050 def validate_reference_in_project(self) -> None: 4051 """Checks if the entered reference protein is valid or not.""" 4052 if len(self._view.ui.txt_new_choose_reference.text()) == 0: 4053 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4054 self._view.ui.lbl_new_status_choose_reference.setText("") 4055 self._view.ui.btn_new_create_project.setEnabled(False) 4056 styles.color_button_not_ready(self._view.ui.btn_new_create_project) 4057 elif len(self._view.ui.txt_new_choose_reference.text()) < 4: 4058 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4059 styles.color_button_not_ready(self._view.ui.btn_new_create_project) 4060 self._view.ui.btn_new_create_project.setEnabled(False) 4061 self._view.ui.lbl_new_status_choose_reference.setText("") 4062 # checks if a pdb id was entered 4063 elif len(self._view.ui.txt_new_choose_reference.text()) == 4: 4064 pdb_id = self._view.ui.txt_new_choose_reference.text().upper() 4065 try: 4066 # the pdb file gets saved in a scratch directory where it gets deleted immediately 4067 cmd.fetch(pdb_id, type="pdb", path=constants.SCRATCH_DIR) 4068 os.remove(f"{constants.SCRATCH_DIR}/{pdb_id}.pdb") 4069 cmd.reinitialize() 4070 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #000000") 4071 self._view.ui.btn_new_create_project.setEnabled(True) 4072 # if the id does not exist an exception gets raised 4073 except pymol.CmdException: 4074 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4075 return 4076 except FileNotFoundError: 4077 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4078 self._view.ui.lbl_new_status_choose_reference.setText("Invalid PDB ID.") 4079 self._view.ui.btn_new_create_project.setEnabled(False) 4080 return 4081 else: 4082 if self._view.ui.txt_new_choose_reference.text().find("/") == -1: 4083 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4084 self._view.ui.btn_new_create_project.setEnabled(False) 4085 styles.color_button_not_ready(self._view.ui.btn_new_create_project) 4086 4087 elif self._view.ui.txt_new_choose_reference.text().find("\\") == -1: 4088 self._view.ui.txt_new_choose_reference.setStyleSheet("color: #FC5457") 4089 self._view.ui.btn_new_create_project.setEnabled(False) 4090 styles.color_button_not_ready(self._view.ui.btn_new_create_project)
Checks if the entered reference protein is valid or not.
def
validate_project_name(self) -> None:
4092 def validate_project_name(self) -> None: 4093 """Validates the input of the project name in real-time.""" 4094 input_validator.InputValidator.validate_project_name( 4095 self._view.ui.list_new_projects, 4096 self._view.ui.txt_new_project_name, 4097 self._view.ui.lbl_new_status_project_name, 4098 self._view.ui.btn_new_create_project, 4099 self._view.ui.cb_new_add_reference, 4100 )
Validates the input of the project name in real-time.
def
validate_open_search(self) -> None:
4105 def validate_open_search(self) -> None: 4106 """Validates the input of the project name in real-time.""" 4107 if self._view.ui.list_open_projects.currentItem() is not None: 4108 self._view.ui.list_open_projects.currentItem().setSelected(False) 4109 # set color for lineEdit 4110 input_validator.InputValidator.validate_search_input( 4111 self._view.ui.list_open_projects, 4112 self._view.ui.txt_open_search, 4113 self._view.ui.lbl_open_status_search, 4114 self._view.ui.txt_open_selected_project, 4115 )
Validates the input of the project name in real-time.
def
select_project_from_open_list(self) -> None:
4117 def select_project_from_open_list(self) -> None: 4118 """Sets the selected project name in the text box.""" 4119 try: 4120 self._view.ui.txt_open_selected_project.setText(self._view.ui.list_open_projects.currentItem().text()) 4121 except AttributeError: 4122 self._view.ui.txt_open_selected_project.setText("")
Sets the selected project name in the text box.
def
select_project_from_delete_list(self) -> None:
4134 def select_project_from_delete_list(self) -> None: 4135 """Selects a project from the project list on the delete page.""" 4136 try: 4137 self._view.ui.txt_delete_selected_projects.setText(self._view.ui.list_delete_projects.currentItem().text()) 4138 except AttributeError: 4139 self._view.ui.txt_delete_selected_projects.setText("")
Selects a project from the project list on the delete page.
def
validate_delete_search(self) -> None:
4148 def validate_delete_search(self) -> None: 4149 """Validates the input of the project name in real-time.""" 4150 if self._view.ui.list_delete_projects.currentItem() is not None: 4151 self._view.ui.list_delete_projects.currentItem().setSelected(False) 4152 # set color for lineEdit 4153 input_validator.InputValidator.validate_search_input( 4154 self._view.ui.list_delete_projects, 4155 self._view.ui.txt_delete_search, 4156 self._view.ui.lbl_delete_status_search, 4157 self._view.ui.txt_delete_selected_projects, 4158 )
Validates the input of the project name in real-time.
def
display_view_page(self) -> None:
4163 def display_view_page(self) -> None: 4164 """Displays the edit project page.""" 4165 if self.is_distance_plot_open: 4166 self.distance_plot_dialog.close() 4167 self.is_distance_plot_open = False 4168 self._view.ui.list_view_project_proteins.clear() 4169 self._view.ui.txtedit_view_sequence.clear() 4170 # pre-process 4171 self._view.status_bar.showMessage(self._workspace_label.text()) 4172 # list all proteins from pdb directory 4173 gui_utils.fill_list_view_with_protein_names(self._current_project, self._view.ui.list_view_project_proteins) 4174 4175 tools.switch_page( 4176 self._view.ui.stackedWidget, 4177 self._view.ui.lbl_page_title, 4178 11, 4179 "View proteins of current project", 4180 ) 4181 self.last_sidebar_button = styles.color_sidebar_buttons(self.last_sidebar_button, self._view.ui.btn_view_page) 4182 gui_elements_to_hide = [ 4183 self._view.ui.btn_view_project_show, 4184 self._view.ui.btn_view_project_show_structure, 4185 self._view.ui.txtedit_view_sequence, 4186 self._view.ui.label_9, 4187 self._view.ui.label_11, 4188 ] 4189 gui_utils.hide_gui_elements(gui_elements_to_hide)
Displays the edit project page.
def
view_show_options(self) -> None:
4191 def view_show_options(self) -> None: 4192 """Controls which gui elements get shown.""" 4193 gui_elements_to_show = [ 4194 # self._view.ui.btn_view_project_show, 4195 self._view.ui.btn_view_project_show_structure, 4196 self._view.ui.txtedit_view_sequence, 4197 # self._view.ui.label_9, 4198 self._view.ui.label_11, 4199 ] 4200 gui_utils.show_gui_elements(gui_elements_to_show) 4201 self.view_sequence()
Controls which gui elements get shown.
def
view_sequence(self) -> None:
4203 def view_sequence(self) -> None: 4204 """Displays the sequence of the selected protein in a text box.""" 4205 tmp_protein_basename = self._view.ui.list_view_project_proteins.currentItem().text() 4206 tmp_protein_sequences = self._current_project.search_protein(tmp_protein_basename).get_protein_sequences() 4207 self._view.ui.txtedit_view_sequence.clear() 4208 for tmp_sequence in tmp_protein_sequences: 4209 self._view.ui.txtedit_view_sequence.append("".join(tmp_sequence.sequence)) 4210 # fixme: experimental sequence viewer gui 4211 # dialog = dialog_sequence_viewer.SequenceViewer(tmp_protein_sequences, tmp_protein_filename) 4212 # dialog.exec_()
Displays the sequence of the selected protein in a text box.
def
validate_use_project_name(self) -> None:
4217 def validate_use_project_name(self) -> None: 4218 """Validates the input of the project name in real-time.""" 4219 input_validator.InputValidator.validate_project_name( 4220 self._view.ui.list_use_existing_projects, 4221 self._view.ui.txt_use_project_name, 4222 self._view.ui.lbl_use_status_project_name, 4223 self._view.ui.btn_use_next, 4224 )
Validates the input of the project name in real-time.
def
validate_use_search(self) -> None:
4226 def validate_use_search(self) -> None: 4227 """Validates the input of the protein name in real-time.""" 4228 message = "Protein structure does not exists." 4229 input_validator.InputValidator.validate_search_input( 4230 self._view.ui.list_use_available_protein_structures, 4231 self._view.ui.txt_use_search, 4232 self._view.ui.lbl_use_status_search, 4233 status_message=message, 4234 )
Validates the input of the protein name in real-time.
def
add_protein_structure_to_new_project(self) -> None:
4236 def add_protein_structure_to_new_project(self) -> None: 4237 """Adds the selected protein to the list which is used to create the new project.""" 4238 prot_to_add = self._view.ui.list_use_available_protein_structures.currentItem().text() 4239 self._view.ui.list_use_selected_protein_structures.addItem(prot_to_add) 4240 self._view.ui.list_use_available_protein_structures.takeItem( 4241 self._view.ui.list_use_available_protein_structures.currentRow(), 4242 ) 4243 self._view.ui.btn_use_add_available_protein_structures.setEnabled(False) 4244 if self._view.ui.list_use_available_protein_structures.count() > 0: 4245 try: 4246 self._view.ui.list_use_available_protein_structures.currentItem().setSelected(False) 4247 except AttributeError: 4248 constants.PYSSA_LOGGER.debug("No selection in use available proteins list on Use page.")
Adds the selected protein to the list which is used to create the new project.
def
remove_protein_structure_to_new_project(self) -> None:
4250 def remove_protein_structure_to_new_project(self) -> None: 4251 """Removes the selected protein from the list which is used to create the new project.""" 4252 prot_to_remove = self._view.ui.list_use_selected_protein_structures.currentItem() 4253 self._view.ui.list_use_selected_protein_structures.takeItem( 4254 self._view.ui.list_use_selected_protein_structures.currentRow(), 4255 ) 4256 self._view.ui.list_use_available_protein_structures.addItem(prot_to_remove) 4257 self._view.ui.btn_use_remove_selected_protein_structures.setEnabled(False) 4258 if self._view.ui.list_use_selected_protein_structures.count() > 0: 4259 try: 4260 self._view.ui.list_use_selected_protein_structures.currentItem().setSelected(False) 4261 except AttributeError: 4262 constants.PYSSA_LOGGER.debug("No selection in use selected proteins list on Use page.")
Removes the selected protein from the list which is used to create the new project.
def
show_protein_selection_for_use(self) -> None:
4264 def show_protein_selection_for_use(self) -> None: 4265 """Shows the two lists for the protein selection.""" 4266 gui_elements_to_show = [ 4267 self._view.ui.lbl_use_search, 4268 self._view.ui.lbl_use_status_search, 4269 self._view.ui.txt_use_search, 4270 self._view.ui.btn_use_add_available_protein_structures, 4271 self._view.ui.lbl_use_available_protein_structures, 4272 self._view.ui.list_use_available_protein_structures, 4273 self._view.ui.btn_use_remove_selected_protein_structures, 4274 self._view.ui.lbl_use_selected_protein_structures, 4275 self._view.ui.list_use_selected_protein_structures, 4276 self._view.ui.btn_use_back, 4277 self._view.ui.btn_use_create_new_project, 4278 self._view.ui.lbl_use_new_project, 4279 ] 4280 gui_utils.show_gui_elements(gui_elements_to_show) 4281 self._view.ui.txt_use_project_name.setEnabled(False) 4282 gui_elements_to_hide = [ 4283 self._view.ui.btn_use_next, 4284 self._view.ui.list_use_existing_projects, 4285 ] 4286 gui_utils.hide_gui_elements(gui_elements_to_hide) 4287 gui_utils.disable_text_box(self._view.ui.txt_use_project_name, self._view.ui.lbl_use_project_name) 4288 self._view.ui.btn_use_add_available_protein_structures.setEnabled(False) 4289 self._view.ui.btn_use_remove_selected_protein_structures.setEnabled(False)
Shows the two lists for the protein selection.
def
hide_protein_selection_for_use(self) -> None:
4291 def hide_protein_selection_for_use(self) -> None: 4292 """Hides the two lists for the protein selection.""" 4293 gui_elements_to_show = [ 4294 self._view.ui.btn_use_next, 4295 self._view.ui.list_use_existing_projects, 4296 ] 4297 gui_utils.show_gui_elements(gui_elements_to_show) 4298 self._view.ui.txt_use_project_name.setEnabled(True) 4299 4300 gui_elements_to_hide = [ 4301 self._view.ui.lbl_use_search, 4302 self._view.ui.lbl_use_status_search, 4303 self._view.ui.txt_use_search, 4304 self._view.ui.btn_use_add_available_protein_structures, 4305 self._view.ui.lbl_use_available_protein_structures, 4306 self._view.ui.list_use_available_protein_structures, 4307 self._view.ui.btn_use_remove_selected_protein_structures, 4308 self._view.ui.lbl_use_selected_protein_structures, 4309 self._view.ui.list_use_selected_protein_structures, 4310 self._view.ui.btn_use_back, 4311 self._view.ui.btn_use_create_new_project, 4312 self._view.ui.lbl_use_new_project, 4313 ] 4314 gui_utils.hide_gui_elements(gui_elements_to_hide) 4315 gui_utils.enable_text_box(self._view.ui.txt_use_project_name, self._view.ui.lbl_use_project_name)
Hides the two lists for the protein selection.
def
use_enable_add(self) -> None:
4317 def use_enable_add(self) -> None: 4318 """Enables the add button.""" 4319 self._view.ui.btn_use_add_available_protein_structures.setEnabled(True)
Enables the add button.
def
use_enable_remove(self) -> None:
4321 def use_enable_remove(self) -> None: 4322 """Enables the remove button.""" 4323 self._view.ui.btn_use_remove_selected_protein_structures.setEnabled(True)
Enables the remove button.
def
display_esm_pred_mono(self) -> None:
4341 def display_esm_pred_mono(self) -> None: 4342 """Displays the esm_fold monomer page.""" 4343 self._init_esm_pred_mono_page() 4344 gui_elements_to_show = [ 4345 self._view.ui.lbl_esm_prot_to_predict, 4346 self._view.ui.table_esm_prot_to_predict, 4347 self._view.ui.btn_esm_seq_to_predict, 4348 ] 4349 gui_elements_to_hide = [ 4350 self._view.ui.btn_esm_seq_to_predict_remove, 4351 self._view.ui.lbl_esm_prot_name, 4352 self._view.ui.txt_esm_prot_name, 4353 self._view.ui.lbl_esm_prot_name_status, 4354 self._view.ui.btn_esm_back, 4355 self._view.ui.btn_esm_next, 4356 self._view.ui.lbl_esm_prot_seq, 4357 self._view.ui.txt_esm_prot_seq, 4358 self._view.ui.lbl_esm_prot_seq_status, 4359 self._view.ui.btn_esm_back_2, 4360 self._view.ui.btn_esm_next_2, 4361 self._view.ui.btn_esm_predict, 4362 ] 4363 gui_utils.show_gui_elements(gui_elements_to_show) 4364 gui_utils.hide_gui_elements(gui_elements_to_hide) 4365 styles.color_button_not_ready(self._view.ui.btn_esm_next) 4366 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 1, "ESMFold Monomer Prediction") 4367 self.last_sidebar_button = styles.color_sidebar_buttons( 4368 self.last_sidebar_button, 4369 self._view.ui.btn_pred_cloud_monomer_page, 4370 )
Displays the esm_fold monomer page.
def
cloud_esm_validate_protein_name(self) -> None:
4372 def cloud_esm_validate_protein_name(self) -> None: 4373 """Validates the input of the protein name in real-time.""" 4374 if safeguard.Safeguard.check_if_value_is_in_table_v_header( 4375 self._view.ui.txt_esm_prot_name.text(), 4376 self._view.ui.table_esm_prot_to_predict, 4377 ): 4378 self._view.ui.lbl_esm_prot_name_status.setText("Protein name already used.") 4379 self._view.ui.btn_esm_next.setEnabled(False) 4380 styles.color_button_not_ready(self._view.ui.btn_esm_next) 4381 else: 4382 self._view.ui.btn_esm_next.setEnabled(True) 4383 tools.validate_protein_name( 4384 self._view.ui.txt_esm_prot_name, 4385 self._view.ui.lbl_esm_prot_name_status, 4386 self._view.ui.btn_esm_next, 4387 )
Validates the input of the protein name in real-time.
def
cloud_esm_validate_protein_sequence(self) -> None:
4389 def cloud_esm_validate_protein_sequence(self) -> None: 4390 """Validates the input of the protein sequence in real-time.""" 4391 tools.validate_protein_sequence( 4392 self._view.ui.txt_esm_prot_seq, 4393 self._view.ui.lbl_esm_prot_seq_status, 4394 self._view.ui.btn_esm_next_2, 4395 )
Validates the input of the protein sequence in real-time.
def
setup_defaults_esm_monomer_prediction(self) -> None:
4397 def setup_defaults_esm_monomer_prediction(self) -> None: 4398 """Sets up the default values for the page.""" 4399 # clears everything 4400 self._view.ui.txt_esm_prot_name.clear() 4401 self._view.ui.txt_esm_prot_seq.clear() 4402 # sets up defaults: Prediction 4403 self._view.ui.btn_esm_next.setEnabled(False) 4404 self._view.ui.btn_esm_next_2.setEnabled(False) 4405 self._view.ui.lbl_esm_prot_name_status.setText("") 4406 self._view.ui.lbl_esm_prot_seq_status.setText("")
Sets up the default values for the page.
def
cloud_esm_add_seq_to_predict(self) -> None:
4408 def cloud_esm_add_seq_to_predict(self) -> None: 4409 """Shows the gui elements to add a sequence to the protein to predict.""" 4410 gui_elements_to_show = [ 4411 self._view.ui.lbl_esm_prot_to_predict, 4412 self._view.ui.table_esm_prot_to_predict, 4413 self._view.ui.lbl_esm_prot_name, 4414 self._view.ui.txt_esm_prot_name, 4415 self._view.ui.lbl_esm_prot_name_status, 4416 self._view.ui.btn_esm_back, 4417 self._view.ui.btn_esm_next, 4418 ] 4419 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4420 gui_elements_to_hide = [ 4421 self._view.ui.btn_esm_seq_to_predict_remove, 4422 self._view.ui.btn_esm_seq_to_predict, 4423 self._view.ui.lbl_esm_prot_seq, 4424 self._view.ui.txt_esm_prot_seq, 4425 self._view.ui.lbl_esm_prot_seq_status, 4426 self._view.ui.btn_esm_back_2, 4427 self._view.ui.btn_esm_next_2, 4428 self._view.ui.btn_esm_predict, 4429 ] 4430 gui_utils.disable_text_box(self._view.ui.txt_esm_prot_seq, self._view.ui.lbl_esm_prot_seq) 4431 gui_utils.show_gui_elements(gui_elements_to_show) 4432 gui_utils.hide_gui_elements(gui_elements_to_hide) 4433 self._view.ui.btn_esm_next.setEnabled(False) 4434 self._view.ui.txt_esm_prot_name.clear() 4435 styles.color_button_not_ready(self._view.ui.btn_esm_next) 4436 if self._view.ui.table_esm_prot_to_predict.rowCount() > 0: 4437 try: 4438 self._view.ui.table_esm_prot_to_predict.currentItem().setSelected(False) 4439 except AttributeError: 4440 constants.PYSSA_LOGGER.debug("No selection on Local Monomer Prediction in overview table.")
Shows the gui elements to add a sequence to the protein to predict.
def
cloud_esm_back(self) -> None:
4442 def cloud_esm_back(self) -> None: 4443 """Hides the gui elements for the protein name.""" 4444 gui_elements_to_show = [ 4445 self._view.ui.lbl_esm_prot_to_predict, 4446 self._view.ui.table_esm_prot_to_predict, 4447 self._view.ui.btn_esm_seq_to_predict_remove, 4448 self._view.ui.btn_esm_seq_to_predict, 4449 ] 4450 gui_elements_to_hide = [ 4451 self._view.ui.lbl_esm_prot_name, 4452 self._view.ui.txt_esm_prot_name, 4453 self._view.ui.lbl_esm_prot_name_status, 4454 self._view.ui.btn_esm_back, 4455 self._view.ui.btn_esm_next, 4456 self._view.ui.lbl_esm_prot_seq, 4457 self._view.ui.txt_esm_prot_seq, 4458 self._view.ui.lbl_esm_prot_seq_status, 4459 self._view.ui.btn_esm_back_2, 4460 self._view.ui.btn_esm_next_2, 4461 self._view.ui.btn_esm_predict, 4462 ] 4463 gui_utils.show_gui_elements(gui_elements_to_show) 4464 gui_utils.hide_gui_elements(gui_elements_to_hide) 4465 self.cloud_esm_check_if_table_is_empty() 4466 self._view.ui.btn_esm_seq_to_predict_remove.setEnabled(False)
Hides the gui elements for the protein name.
def
cloud_esm_next(self) -> None:
4468 def cloud_esm_next(self) -> None: 4469 """Shows the gui elements for the protein name.""" 4470 gui_elements_to_show = [ 4471 self._view.ui.lbl_esm_prot_to_predict, 4472 self._view.ui.table_esm_prot_to_predict, 4473 self._view.ui.lbl_esm_prot_name, 4474 self._view.ui.txt_esm_prot_name, 4475 self._view.ui.lbl_esm_prot_seq, 4476 self._view.ui.txt_esm_prot_seq, 4477 self._view.ui.lbl_esm_prot_seq_status, 4478 self._view.ui.btn_esm_back_2, 4479 self._view.ui.btn_esm_next_2, 4480 ] 4481 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_seq, self._view.ui.lbl_esm_prot_seq) 4482 gui_elements_to_hide = [ 4483 self._view.ui.btn_esm_seq_to_predict_remove, 4484 self._view.ui.btn_esm_seq_to_predict, 4485 self._view.ui.lbl_esm_prot_name_status, 4486 self._view.ui.btn_esm_back, 4487 self._view.ui.btn_esm_next, 4488 self._view.ui.btn_esm_predict, 4489 ] 4490 gui_utils.disable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4491 gui_utils.show_gui_elements(gui_elements_to_show) 4492 gui_utils.hide_gui_elements(gui_elements_to_hide) 4493 self._view.ui.txt_esm_prot_seq.clear()
Shows the gui elements for the protein name.
def
cloud_esm_back_2(self) -> None:
4495 def cloud_esm_back_2(self) -> None: 4496 """Hides the gui elements for the protein sequence.""" 4497 gui_elements_to_show = [ 4498 self._view.ui.lbl_esm_prot_to_predict, 4499 self._view.ui.table_esm_prot_to_predict, 4500 self._view.ui.lbl_esm_prot_name, 4501 self._view.ui.txt_esm_prot_name, 4502 self._view.ui.lbl_esm_prot_name_status, 4503 self._view.ui.btn_esm_back, 4504 self._view.ui.btn_esm_next, 4505 ] 4506 gui_elements_to_hide = [ 4507 self._view.ui.btn_esm_seq_to_predict_remove, 4508 self._view.ui.btn_esm_seq_to_predict, 4509 self._view.ui.lbl_esm_prot_seq, 4510 self._view.ui.txt_esm_prot_seq, 4511 self._view.ui.lbl_esm_prot_seq_status, 4512 self._view.ui.btn_esm_back_2, 4513 self._view.ui.btn_esm_next_2, 4514 self._view.ui.btn_esm_predict, 4515 ] 4516 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4517 gui_utils.disable_text_box(self._view.ui.txt_esm_prot_seq, self._view.ui.lbl_esm_prot_seq) 4518 gui_utils.show_gui_elements(gui_elements_to_show) 4519 gui_utils.hide_gui_elements(gui_elements_to_hide)
Hides the gui elements for the protein sequence.
def
cloud_esm_add_protein(self) -> None:
4521 def cloud_esm_add_protein(self) -> None: 4522 """Adds protein to the list of proteins to predict.""" 4523 self._view.ui.table_esm_prot_to_predict.setRowCount(self._view.ui.table_esm_prot_to_predict.rowCount() + 1) 4524 self._view.ui.table_esm_prot_to_predict.insertRow(self._view.ui.table_esm_prot_to_predict.rowCount() + 1) 4525 self._view.ui.table_esm_prot_to_predict.setItem( 4526 self._view.ui.table_esm_prot_to_predict.rowCount() - 1, 4527 0, 4528 QtWidgets.QTableWidgetItem("A"), 4529 ) 4530 self._view.ui.table_esm_prot_to_predict.setItem( 4531 self._view.ui.table_esm_prot_to_predict.rowCount() - 1, 4532 1, 4533 QtWidgets.QTableWidgetItem(self._view.ui.txt_esm_prot_seq.toPlainText()), 4534 ) 4535 self._view.ui.table_esm_prot_to_predict.setVerticalHeaderItem( 4536 self._view.ui.table_esm_prot_to_predict.rowCount() - 1, 4537 QtWidgets.QTableWidgetItem(self._view.ui.txt_esm_prot_name.text()), 4538 ) 4539 self._view.ui.table_esm_prot_to_predict.resizeColumnsToContents() 4540 self.cloud_esm_check_if_table_is_empty() 4541 gui_elements_to_show = [ 4542 self._view.ui.lbl_esm_prot_to_predict, 4543 self._view.ui.table_esm_prot_to_predict, 4544 self._view.ui.btn_esm_seq_to_predict_remove, 4545 self._view.ui.btn_esm_seq_to_predict, 4546 self._view.ui.btn_esm_predict, 4547 ] 4548 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4549 gui_elements_to_hide = [ 4550 self._view.ui.lbl_esm_prot_name, 4551 self._view.ui.txt_esm_prot_name, 4552 self._view.ui.lbl_esm_prot_name_status, 4553 self._view.ui.btn_esm_back, 4554 self._view.ui.btn_esm_next, 4555 self._view.ui.lbl_esm_prot_seq, 4556 self._view.ui.txt_esm_prot_seq, 4557 self._view.ui.lbl_esm_prot_seq_status, 4558 self._view.ui.btn_esm_back_2, 4559 self._view.ui.btn_esm_next_2, 4560 ] 4561 gui_utils.show_gui_elements(gui_elements_to_show) 4562 gui_utils.hide_gui_elements(gui_elements_to_hide) 4563 self._view.ui.btn_esm_predict.setEnabled(True) 4564 self._view.ui.btn_esm_seq_to_predict_remove.setEnabled(False) 4565 self.setup_defaults_esm_monomer_prediction()
Adds protein to the list of proteins to predict.
def
cloud_esm_remove(self) -> None:
4567 def cloud_esm_remove(self) -> None: 4568 """Removes a protein from the list of proteins to predict.""" 4569 self._view.ui.table_esm_prot_to_predict.removeRow(self._view.ui.table_esm_prot_to_predict.currentRow()) 4570 gui_elements_to_show = [ 4571 self._view.ui.lbl_esm_prot_to_predict, 4572 self._view.ui.table_esm_prot_to_predict, 4573 self._view.ui.btn_esm_seq_to_predict_remove, 4574 self._view.ui.btn_esm_seq_to_predict, 4575 self._view.ui.btn_esm_predict, 4576 ] 4577 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4578 gui_elements_to_hide = [ 4579 self._view.ui.lbl_esm_prot_name, 4580 self._view.ui.txt_esm_prot_name, 4581 self._view.ui.lbl_esm_prot_name_status, 4582 self._view.ui.btn_esm_back, 4583 self._view.ui.btn_esm_next, 4584 self._view.ui.lbl_esm_prot_seq, 4585 self._view.ui.txt_esm_prot_seq, 4586 self._view.ui.lbl_esm_prot_seq_status, 4587 self._view.ui.btn_esm_back_2, 4588 self._view.ui.btn_esm_next_2, 4589 ] 4590 gui_utils.show_gui_elements(gui_elements_to_show) 4591 gui_utils.hide_gui_elements(gui_elements_to_hide) 4592 self._view.ui.btn_esm_seq_to_predict_remove.setEnabled(False) 4593 self.cloud_esm_check_if_table_is_empty()
Removes a protein from the list of proteins to predict.
def
cloud_esm_item_changed(self) -> None:
4595 def cloud_esm_item_changed(self) -> None: 4596 """Enables the remove button.""" 4597 self._view.ui.btn_esm_seq_to_predict_remove.setEnabled(True)
Enables the remove button.
def
cloud_esm_check_if_table_is_empty(self) -> None:
4599 def cloud_esm_check_if_table_is_empty(self) -> None: 4600 """Checks if the table proteins to predict is empty.""" 4601 if self._view.ui.table_esm_prot_to_predict.rowCount() == 0: 4602 styles.color_button_not_ready(self._view.ui.btn_esm_predict) 4603 self._view.ui.btn_esm_predict.setEnabled(False) 4604 gui_elements_to_show = [ 4605 self._view.ui.lbl_esm_prot_to_predict, 4606 self._view.ui.table_esm_prot_to_predict, 4607 self._view.ui.btn_esm_seq_to_predict, 4608 ] 4609 gui_utils.enable_text_box(self._view.ui.txt_esm_prot_name, self._view.ui.lbl_esm_prot_name) 4610 gui_elements_to_hide = [ 4611 self._view.ui.btn_esm_seq_to_predict_remove, 4612 self._view.ui.lbl_esm_prot_name, 4613 self._view.ui.txt_esm_prot_name, 4614 self._view.ui.lbl_esm_prot_name_status, 4615 self._view.ui.btn_esm_back, 4616 self._view.ui.btn_esm_next, 4617 self._view.ui.lbl_esm_prot_seq, 4618 self._view.ui.txt_esm_prot_seq, 4619 self._view.ui.lbl_esm_prot_seq_status, 4620 self._view.ui.btn_esm_back_2, 4621 self._view.ui.btn_esm_next_2, 4622 self._view.ui.btn_esm_predict, 4623 ] 4624 gui_utils.show_gui_elements(gui_elements_to_show) 4625 gui_utils.hide_gui_elements(gui_elements_to_hide) 4626 else: 4627 self._view.ui.btn_esm_predict.setEnabled(True)
Checks if the table proteins to predict is empty.
def
display_local_pred_mono(self) -> None:
4645 def display_local_pred_mono(self) -> None: 4646 """Displays the local prediction monomer page.""" 4647 # checks internet connection 4648 if not tools.check_internet_connectivity(): 4649 gui_utils.no_internet_dialog() 4650 return 4651 self._init_local_pred_mono_page() 4652 gui_elements_to_show = [ 4653 self._view.ui.lbl_pred_mono_prot_to_predict, 4654 self._view.ui.table_pred_mono_prot_to_predict, 4655 self._view.ui.btn_pred_mono_seq_to_predict, 4656 ] 4657 gui_elements_to_hide = [ 4658 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4659 self._view.ui.lbl_pred_mono_prot_name, 4660 self._view.ui.txt_pred_mono_prot_name, 4661 self._view.ui.lbl_pred_mono_prot_name_status, 4662 self._view.ui.btn_pred_mono_back, 4663 self._view.ui.btn_pred_mono_next, 4664 self._view.ui.lbl_pred_mono_seq_name, 4665 self._view.ui.txt_pred_mono_seq_name, 4666 self._view.ui.lbl_pred_mono_seq_name_status, 4667 self._view.ui.btn_pred_mono_back_2, 4668 self._view.ui.btn_pred_mono_add_protein, 4669 self._view.ui.lbl_pred_mono_advanced_config, 4670 self._view.ui.btn_pred_mono_advanced_config, 4671 self._view.ui.btn_pred_mono_predict, 4672 ] 4673 gui_utils.show_gui_elements(gui_elements_to_show) 4674 gui_utils.hide_gui_elements(gui_elements_to_hide) 4675 styles.color_button_not_ready(self._view.ui.btn_pred_mono_next) 4676 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 19, "Local Monomer Prediction") 4677 self.last_sidebar_button = styles.color_sidebar_buttons( 4678 self.last_sidebar_button, 4679 self._view.ui.btn_pred_local_monomer_page, 4680 )
Displays the local prediction monomer page.
def
local_pred_mono_validate_protein_name(self) -> None:
4682 def local_pred_mono_validate_protein_name(self) -> None: 4683 """Validates the input of the protein name in real-time.""" 4684 if safeguard.Safeguard.check_if_value_is_in_table_v_header( 4685 self._view.ui.txt_pred_mono_prot_name.text(), 4686 self._view.ui.table_pred_mono_prot_to_predict, 4687 ): 4688 self._view.ui.lbl_pred_mono_prot_name_status.setText("Protein name already used.") 4689 self._view.ui.btn_pred_mono_next.setEnabled(False) 4690 styles.color_button_not_ready(self._view.ui.btn_pred_mono_next) 4691 else: 4692 self._view.ui.btn_pred_mono_next.setEnabled(True) 4693 tools.validate_protein_name( 4694 self._view.ui.txt_pred_mono_prot_name, 4695 self._view.ui.lbl_pred_mono_prot_name_status, 4696 self._view.ui.btn_pred_mono_next, 4697 )
Validates the input of the protein name in real-time.
def
local_pred_mono_validate_protein_sequence(self) -> None:
4699 def local_pred_mono_validate_protein_sequence(self) -> None: 4700 """Validates the input of the protein sequence in real-time.""" 4701 tools.validate_protein_sequence( 4702 self._view.ui.txt_pred_mono_seq_name, 4703 self._view.ui.lbl_pred_mono_seq_name_status, 4704 self._view.ui.btn_pred_mono_add_protein, 4705 )
Validates the input of the protein sequence in real-time.
def
show_prediction_configuration(self) -> None:
4707 def show_prediction_configuration(self) -> None: 4708 """Opens the prediction configuration dialog window.""" 4709 config = dialog_advanced_prediction_configurations.DialogAdvancedPredictionConfigurations( 4710 self.prediction_configuration, 4711 ) 4712 config.exec_() 4713 self.prediction_configuration.amber_force_field = config.prediction_config.amber_force_field 4714 self.prediction_configuration.templates = config.prediction_config.templates
Opens the prediction configuration dialog window.
def
setup_defaults_monomer_prediction(self) -> None:
4716 def setup_defaults_monomer_prediction(self) -> None: 4717 """Sets up the defaults for the page.""" 4718 # clears everything 4719 self._view.ui.txt_pred_mono_prot_name.clear() 4720 self._view.ui.txt_pred_mono_seq_name.clear() 4721 # sets up defaults: Prediction 4722 self._view.ui.btn_pred_mono_next.setEnabled(False) 4723 self._view.ui.btn_pred_mono_add_protein.setEnabled(False) 4724 self._view.ui.lbl_pred_mono_prot_name_status.setText("") 4725 self._view.ui.lbl_pred_mono_seq_name_status.setText("")
Sets up the defaults for the page.
def
local_pred_mono_add_seq_to_predict(self) -> None:
4727 def local_pred_mono_add_seq_to_predict(self) -> None: 4728 """Shows the gui elements for the protein name.""" 4729 gui_elements_to_show = [ 4730 self._view.ui.lbl_pred_mono_prot_to_predict, 4731 self._view.ui.table_pred_mono_prot_to_predict, 4732 self._view.ui.lbl_pred_mono_prot_name, 4733 self._view.ui.txt_pred_mono_prot_name, 4734 self._view.ui.lbl_pred_mono_prot_name_status, 4735 self._view.ui.btn_pred_mono_back, 4736 self._view.ui.btn_pred_mono_next, 4737 ] 4738 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4739 gui_elements_to_hide = [ 4740 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4741 self._view.ui.btn_pred_mono_seq_to_predict, 4742 self._view.ui.lbl_pred_mono_seq_name, 4743 self._view.ui.txt_pred_mono_seq_name, 4744 self._view.ui.lbl_pred_mono_seq_name_status, 4745 self._view.ui.btn_pred_mono_back_2, 4746 self._view.ui.btn_pred_mono_add_protein, 4747 self._view.ui.lbl_pred_mono_advanced_config, 4748 self._view.ui.btn_pred_mono_advanced_config, 4749 self._view.ui.btn_pred_mono_predict, 4750 ] 4751 gui_utils.disable_text_box(self._view.ui.txt_pred_mono_seq_name, self._view.ui.lbl_pred_mono_seq_name) 4752 gui_utils.show_gui_elements(gui_elements_to_show) 4753 gui_utils.hide_gui_elements(gui_elements_to_hide) 4754 self._view.ui.btn_pred_mono_next.setEnabled(False) 4755 self._view.ui.txt_pred_mono_prot_name.clear() 4756 styles.color_button_not_ready(self._view.ui.btn_pred_mono_next) 4757 if self._view.ui.table_pred_mono_prot_to_predict.rowCount() > 0: 4758 try: 4759 self._view.ui.table_pred_mono_prot_to_predict.currentItem().setSelected(False) 4760 except AttributeError: 4761 constants.PYSSA_LOGGER.debug("No selection on Local Monomer Prediction in overview table.")
Shows the gui elements for the protein name.
def
local_pred_mono_back(self) -> None:
4763 def local_pred_mono_back(self) -> None: 4764 """Hides the gui elements for the protein name.""" 4765 gui_elements_to_show = [ 4766 self._view.ui.lbl_pred_mono_prot_to_predict, 4767 self._view.ui.table_pred_mono_prot_to_predict, 4768 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4769 self._view.ui.btn_pred_mono_seq_to_predict, 4770 ] 4771 gui_elements_to_hide = [ 4772 self._view.ui.lbl_pred_mono_prot_name, 4773 self._view.ui.txt_pred_mono_prot_name, 4774 self._view.ui.lbl_pred_mono_prot_name_status, 4775 self._view.ui.btn_pred_mono_back, 4776 self._view.ui.btn_pred_mono_next, 4777 self._view.ui.lbl_pred_mono_seq_name, 4778 self._view.ui.txt_pred_mono_seq_name, 4779 self._view.ui.lbl_pred_mono_seq_name_status, 4780 self._view.ui.btn_pred_mono_back_2, 4781 self._view.ui.btn_pred_mono_add_protein, 4782 self._view.ui.lbl_pred_mono_advanced_config, 4783 self._view.ui.btn_pred_mono_advanced_config, 4784 self._view.ui.btn_pred_mono_predict, 4785 ] 4786 gui_utils.show_gui_elements(gui_elements_to_show) 4787 gui_utils.hide_gui_elements(gui_elements_to_hide) 4788 self.local_pred_mono_check_if_table_is_empty() 4789 self._view.ui.btn_pred_mono_seq_to_predict_remove.setEnabled(False)
Hides the gui elements for the protein name.
def
local_pred_mono_next(self) -> None:
4791 def local_pred_mono_next(self) -> None: 4792 """Shows the gui elements for the protein sequence.""" 4793 gui_elements_to_show = [ 4794 self._view.ui.lbl_pred_mono_prot_to_predict, 4795 self._view.ui.table_pred_mono_prot_to_predict, 4796 self._view.ui.lbl_pred_mono_prot_name, 4797 self._view.ui.txt_pred_mono_prot_name, 4798 self._view.ui.lbl_pred_mono_seq_name, 4799 self._view.ui.txt_pred_mono_seq_name, 4800 self._view.ui.lbl_pred_mono_seq_name_status, 4801 self._view.ui.btn_pred_mono_back_2, 4802 self._view.ui.btn_pred_mono_add_protein, 4803 ] 4804 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_seq_name, self._view.ui.lbl_pred_mono_seq_name) 4805 gui_elements_to_hide = [ 4806 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4807 self._view.ui.btn_pred_mono_seq_to_predict, 4808 self._view.ui.lbl_pred_mono_prot_name_status, 4809 self._view.ui.btn_pred_mono_back, 4810 self._view.ui.btn_pred_mono_next, 4811 self._view.ui.lbl_pred_mono_advanced_config, 4812 self._view.ui.btn_pred_mono_advanced_config, 4813 self._view.ui.btn_pred_mono_predict, 4814 ] 4815 gui_utils.disable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4816 gui_utils.show_gui_elements(gui_elements_to_show) 4817 gui_utils.hide_gui_elements(gui_elements_to_hide) 4818 self._view.ui.txt_pred_mono_seq_name.clear()
Shows the gui elements for the protein sequence.
def
local_pred_mono_back_2(self) -> None:
4820 def local_pred_mono_back_2(self) -> None: 4821 """Hides the gui elements for the protein sequence.""" 4822 gui_elements_to_show = [ 4823 self._view.ui.lbl_pred_mono_prot_to_predict, 4824 self._view.ui.table_pred_mono_prot_to_predict, 4825 self._view.ui.lbl_pred_mono_prot_name, 4826 self._view.ui.txt_pred_mono_prot_name, 4827 self._view.ui.lbl_pred_mono_prot_name_status, 4828 self._view.ui.btn_pred_mono_back, 4829 self._view.ui.btn_pred_mono_next, 4830 ] 4831 gui_elements_to_hide = [ 4832 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4833 self._view.ui.btn_pred_mono_seq_to_predict, 4834 self._view.ui.lbl_pred_mono_seq_name, 4835 self._view.ui.txt_pred_mono_seq_name, 4836 self._view.ui.lbl_pred_mono_seq_name_status, 4837 self._view.ui.btn_pred_mono_back_2, 4838 self._view.ui.btn_pred_mono_add_protein, 4839 self._view.ui.lbl_pred_mono_advanced_config, 4840 self._view.ui.btn_pred_mono_advanced_config, 4841 self._view.ui.btn_pred_mono_predict, 4842 ] 4843 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4844 gui_utils.disable_text_box(self._view.ui.txt_pred_mono_seq_name, self._view.ui.lbl_pred_mono_seq_name) 4845 gui_utils.show_gui_elements(gui_elements_to_show) 4846 gui_utils.hide_gui_elements(gui_elements_to_hide)
Hides the gui elements for the protein sequence.
def
local_pred_mono_add_protein(self) -> None:
4848 def local_pred_mono_add_protein(self) -> None: 4849 """Adds protein to the list of proteins to predict.""" 4850 self._view.ui.table_pred_mono_prot_to_predict.setRowCount( 4851 self._view.ui.table_pred_mono_prot_to_predict.rowCount() + 1, 4852 ) 4853 self._view.ui.table_pred_mono_prot_to_predict.insertRow( 4854 self._view.ui.table_pred_mono_prot_to_predict.rowCount() + 1, 4855 ) 4856 self._view.ui.table_pred_mono_prot_to_predict.setItem( 4857 self._view.ui.table_pred_mono_prot_to_predict.rowCount() - 1, 4858 0, 4859 QtWidgets.QTableWidgetItem("A"), 4860 ) 4861 self._view.ui.table_pred_mono_prot_to_predict.setItem( 4862 self._view.ui.table_pred_mono_prot_to_predict.rowCount() - 1, 4863 1, 4864 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_mono_seq_name.toPlainText()), 4865 ) 4866 self._view.ui.table_pred_mono_prot_to_predict.setVerticalHeaderItem( 4867 self._view.ui.table_pred_mono_prot_to_predict.rowCount() - 1, 4868 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_mono_prot_name.text()), 4869 ) 4870 self._view.ui.table_pred_mono_prot_to_predict.resizeColumnsToContents() 4871 self.local_pred_mono_check_if_table_is_empty() 4872 gui_elements_to_show = [ 4873 self._view.ui.lbl_pred_mono_prot_to_predict, 4874 self._view.ui.table_pred_mono_prot_to_predict, 4875 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4876 self._view.ui.btn_pred_mono_seq_to_predict, 4877 self._view.ui.lbl_pred_mono_advanced_config, 4878 self._view.ui.btn_pred_mono_advanced_config, 4879 self._view.ui.btn_pred_mono_predict, 4880 ] 4881 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4882 gui_elements_to_hide = [ 4883 self._view.ui.lbl_pred_mono_prot_name, 4884 self._view.ui.txt_pred_mono_prot_name, 4885 self._view.ui.lbl_pred_mono_prot_name_status, 4886 self._view.ui.btn_pred_mono_back, 4887 self._view.ui.btn_pred_mono_next, 4888 self._view.ui.lbl_pred_mono_seq_name, 4889 self._view.ui.txt_pred_mono_seq_name, 4890 self._view.ui.lbl_pred_mono_seq_name_status, 4891 self._view.ui.btn_pred_mono_back_2, 4892 self._view.ui.btn_pred_mono_add_protein, 4893 ] 4894 gui_utils.show_gui_elements(gui_elements_to_show) 4895 gui_utils.hide_gui_elements(gui_elements_to_hide) 4896 self._view.ui.btn_pred_mono_predict.setEnabled(True) 4897 self._view.ui.btn_pred_mono_seq_to_predict_remove.setEnabled(False) 4898 self.setup_defaults_monomer_prediction()
Adds protein to the list of proteins to predict.
def
local_pred_mono_remove(self) -> None:
4900 def local_pred_mono_remove(self) -> None: 4901 """Removes the selected protein from the list of proteins to predict.""" 4902 self._view.ui.table_pred_mono_prot_to_predict.removeRow( 4903 self._view.ui.table_pred_mono_prot_to_predict.currentRow(), 4904 ) 4905 gui_elements_to_show = [ 4906 self._view.ui.lbl_pred_mono_prot_to_predict, 4907 self._view.ui.table_pred_mono_prot_to_predict, 4908 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4909 self._view.ui.btn_pred_mono_seq_to_predict, 4910 self._view.ui.lbl_pred_mono_advanced_config, 4911 self._view.ui.btn_pred_mono_advanced_config, 4912 self._view.ui.btn_pred_mono_predict, 4913 ] 4914 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4915 gui_elements_to_hide = [ 4916 self._view.ui.lbl_pred_mono_prot_name, 4917 self._view.ui.txt_pred_mono_prot_name, 4918 self._view.ui.lbl_pred_mono_prot_name_status, 4919 self._view.ui.btn_pred_mono_back, 4920 self._view.ui.btn_pred_mono_next, 4921 self._view.ui.lbl_pred_mono_seq_name, 4922 self._view.ui.txt_pred_mono_seq_name, 4923 self._view.ui.lbl_pred_mono_seq_name_status, 4924 self._view.ui.btn_pred_mono_back_2, 4925 self._view.ui.btn_pred_mono_add_protein, 4926 ] 4927 gui_utils.show_gui_elements(gui_elements_to_show) 4928 gui_utils.hide_gui_elements(gui_elements_to_hide) 4929 self._view.ui.btn_pred_mono_seq_to_predict_remove.setEnabled(False) 4930 self.local_pred_mono_check_if_table_is_empty()
Removes the selected protein from the list of proteins to predict.
def
local_pred_mono_item_changed(self) -> None:
4932 def local_pred_mono_item_changed(self) -> None: 4933 """Enables the remove button.""" 4934 self._view.ui.btn_pred_mono_seq_to_predict_remove.setEnabled(True)
Enables the remove button.
def
local_pred_mono_check_if_table_is_empty(self) -> None:
4936 def local_pred_mono_check_if_table_is_empty(self) -> None: 4937 """Checks if the table proteins to predict is empty.""" 4938 if self._view.ui.table_pred_mono_prot_to_predict.rowCount() == 0: 4939 styles.color_button_not_ready(self._view.ui.btn_pred_mono_predict) 4940 self._view.ui.btn_pred_mono_predict.setEnabled(False) 4941 gui_elements_to_show = [ 4942 self._view.ui.lbl_pred_mono_prot_to_predict, 4943 self._view.ui.table_pred_mono_prot_to_predict, 4944 self._view.ui.btn_pred_mono_seq_to_predict, 4945 ] 4946 gui_utils.enable_text_box(self._view.ui.txt_pred_mono_prot_name, self._view.ui.lbl_pred_mono_prot_name) 4947 gui_elements_to_hide = [ 4948 self._view.ui.btn_pred_mono_seq_to_predict_remove, 4949 self._view.ui.lbl_pred_mono_prot_name, 4950 self._view.ui.txt_pred_mono_prot_name, 4951 self._view.ui.lbl_pred_mono_prot_name_status, 4952 self._view.ui.btn_pred_mono_back, 4953 self._view.ui.btn_pred_mono_next, 4954 self._view.ui.lbl_pred_mono_seq_name, 4955 self._view.ui.txt_pred_mono_seq_name, 4956 self._view.ui.lbl_pred_mono_seq_name_status, 4957 self._view.ui.btn_pred_mono_back_2, 4958 self._view.ui.btn_pred_mono_add_protein, 4959 self._view.ui.lbl_pred_mono_advanced_config, 4960 self._view.ui.btn_pred_mono_advanced_config, 4961 self._view.ui.btn_pred_mono_predict, 4962 ] 4963 gui_utils.show_gui_elements(gui_elements_to_show) 4964 gui_utils.hide_gui_elements(gui_elements_to_hide) 4965 else: 4966 self._view.ui.btn_pred_mono_predict.setEnabled(True)
Checks if the table proteins to predict is empty.
def
display_local_pred_multi(self) -> None:
4983 def display_local_pred_multi(self) -> None: 4984 """Displays the local prediction multimer page.""" 4985 # checks internet connection 4986 if not tools.check_internet_connectivity(): 4987 gui_utils.no_internet_dialog() 4988 return 4989 4990 gui_elements_to_show = [ 4991 self._view.ui.lbl_pred_multi_prot_to_predict, 4992 self._view.ui.table_pred_multi_prot_to_predict, 4993 self._view.ui.btn_pred_multi_prot_to_predict_add, 4994 ] 4995 gui_elements_to_hide = [ 4996 self._view.ui.btn_pred_multi_prot_to_predict_remove, 4997 self._view.ui.lbl_pred_multi_prot_name_status, 4998 self._view.ui.btn_pred_multi_back, 4999 self._view.ui.btn_pred_multi_next, 5000 self._view.ui.lbl_pred_multi_prot_name, 5001 self._view.ui.txt_pred_multi_prot_name, 5002 self._view.ui.lbl_pred_multi_prot_seq, 5003 self._view.ui.txt_pred_multi_prot_seq, 5004 self._view.ui.lbl_pred_multi_prot_seq_status, 5005 self._view.ui.lbl_pred_multi_prot_seq_add, 5006 self._view.ui.btn_pred_multi_prot_seq_add, 5007 self._view.ui.lbl_pred_multi_prot_seq_overview, 5008 self._view.ui.list_pred_multi_prot_seq_overview, 5009 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5010 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5011 self._view.ui.btn_pred_multi_back_2, 5012 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5013 self._view.ui.lbl_pred_multi_advanced_config, 5014 self._view.ui.btn_pred_multi_advanced_config, 5015 self._view.ui.btn_pred_multi_predict, 5016 ] 5017 for i in range(self._view.ui.table_pred_multi_prot_to_predict.rowCount() - 1, -1, -1): 5018 self._view.ui.table_pred_multi_prot_to_predict.removeRow(i) 5019 gui_utils.show_gui_elements(gui_elements_to_show) 5020 gui_utils.hide_gui_elements(gui_elements_to_hide) 5021 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 20, "Local Multimer Prediction") 5022 self.last_sidebar_button = styles.color_sidebar_buttons( 5023 self.last_sidebar_button, 5024 self._view.ui.btn_pred_local_multimer_page, 5025 )
Displays the local prediction multimer page.
def
local_pred_multi_validate_protein_name(self) -> None:
5027 def local_pred_multi_validate_protein_name(self) -> None: 5028 """Validates the input of the protein name in real-time.""" 5029 if safeguard.Safeguard.check_if_value_is_in_table_v_header( 5030 self._view.ui.txt_pred_multi_prot_name.text(), 5031 self._view.ui.table_pred_multi_prot_to_predict, 5032 ): 5033 self._view.ui.lbl_pred_multi_prot_name_status.setText("Protein name already used.") 5034 self._view.ui.btn_pred_multi_next.setEnabled(False) 5035 styles.color_button_not_ready(self._view.ui.btn_pred_multi_next) 5036 else: 5037 self._view.ui.btn_pred_multi_next.setEnabled(True) 5038 tools.validate_protein_name( 5039 self._view.ui.txt_pred_multi_prot_name, 5040 self._view.ui.lbl_pred_multi_prot_name_status, 5041 self._view.ui.btn_pred_multi_next, 5042 )
Validates the input of the protein name in real-time.
def
local_pred_multi_validate_protein_sequence(self) -> None:
5044 def local_pred_multi_validate_protein_sequence(self) -> None: 5045 """Validates the input of the protein sequence in real-time.""" 5046 tools.validate_protein_sequence( 5047 self._view.ui.txt_pred_multi_prot_seq, 5048 self._view.ui.lbl_pred_multi_prot_seq_status, 5049 self._view.ui.btn_pred_multi_prot_seq_add, 5050 )
Validates the input of the protein sequence in real-time.
def
local_pred_multi_check_if_table_is_empty(self) -> None:
5052 def local_pred_multi_check_if_table_is_empty(self) -> None: 5053 """Checks if the table proteins to predict is empty.""" 5054 if self._view.ui.table_pred_multi_prot_to_predict.rowCount() == 0: 5055 styles.color_button_not_ready(self._view.ui.btn_pred_multi_predict) 5056 self._view.ui.btn_pred_multi_predict.setEnabled(False) 5057 gui_elements_to_show = [ 5058 self._view.ui.lbl_pred_multi_prot_to_predict, 5059 self._view.ui.table_pred_multi_prot_to_predict, 5060 self._view.ui.btn_pred_multi_prot_to_predict_add, 5061 ] 5062 gui_elements_to_hide = [ 5063 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5064 self._view.ui.lbl_pred_multi_prot_name_status, 5065 self._view.ui.btn_pred_multi_back, 5066 self._view.ui.btn_pred_multi_next, 5067 self._view.ui.lbl_pred_multi_prot_name, 5068 self._view.ui.txt_pred_multi_prot_name, 5069 self._view.ui.lbl_pred_multi_prot_seq, 5070 self._view.ui.txt_pred_multi_prot_seq, 5071 self._view.ui.lbl_pred_multi_prot_seq_status, 5072 self._view.ui.lbl_pred_multi_prot_seq_add, 5073 self._view.ui.btn_pred_multi_prot_seq_add, 5074 self._view.ui.lbl_pred_multi_prot_seq_overview, 5075 self._view.ui.list_pred_multi_prot_seq_overview, 5076 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5077 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5078 self._view.ui.btn_pred_multi_back_2, 5079 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5080 self._view.ui.lbl_pred_multi_advanced_config, 5081 self._view.ui.btn_pred_multi_advanced_config, 5082 self._view.ui.btn_pred_multi_predict, 5083 ] 5084 gui_utils.show_gui_elements(gui_elements_to_show) 5085 gui_utils.hide_gui_elements(gui_elements_to_hide) 5086 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False) 5087 else: 5088 self._view.ui.btn_pred_multi_predict.setEnabled(True) 5089 gui_elements_to_show = [ 5090 self._view.ui.lbl_pred_multi_prot_to_predict, 5091 self._view.ui.table_pred_multi_prot_to_predict, 5092 self._view.ui.btn_pred_multi_prot_to_predict_add, 5093 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5094 self._view.ui.lbl_pred_multi_advanced_config, 5095 self._view.ui.btn_pred_multi_advanced_config, 5096 self._view.ui.btn_pred_multi_predict, 5097 ] 5098 gui_elements_to_hide = [ 5099 self._view.ui.lbl_pred_multi_prot_name_status, 5100 self._view.ui.btn_pred_multi_back, 5101 self._view.ui.btn_pred_multi_next, 5102 self._view.ui.lbl_pred_multi_prot_name, 5103 self._view.ui.txt_pred_multi_prot_name, 5104 self._view.ui.lbl_pred_multi_prot_seq, 5105 self._view.ui.txt_pred_multi_prot_seq, 5106 self._view.ui.lbl_pred_multi_prot_seq_status, 5107 self._view.ui.lbl_pred_multi_prot_seq_add, 5108 self._view.ui.btn_pred_multi_prot_seq_add, 5109 self._view.ui.lbl_pred_multi_prot_seq_overview, 5110 self._view.ui.list_pred_multi_prot_seq_overview, 5111 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5112 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5113 self._view.ui.btn_pred_multi_back_2, 5114 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5115 ] 5116 gui_utils.show_gui_elements(gui_elements_to_show) 5117 gui_utils.hide_gui_elements(gui_elements_to_hide) 5118 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False)
Checks if the table proteins to predict is empty.
def
local_pred_multi_add_sequence_to_list(self) -> None:
5120 def local_pred_multi_add_sequence_to_list(self) -> None: 5121 """Adds the entered sequence to the list of sequences of the protein.""" 5122 self._view.ui.list_pred_multi_prot_seq_overview.addItem( 5123 QtWidgets.QListWidgetItem(self._view.ui.txt_pred_multi_prot_seq.toPlainText()), 5124 ) 5125 self.local_pred_multi_check_if_list_is_empty()
Adds the entered sequence to the list of sequences of the protein.
def
local_pred_multi_remove_sequence_to_list(self) -> None:
5127 def local_pred_multi_remove_sequence_to_list(self) -> None: 5128 """Removes the entered sequence to the list of sequences of the protein.""" 5129 self._view.ui.list_pred_multi_prot_seq_overview.takeItem( 5130 self._view.ui.list_pred_multi_prot_seq_overview.currentRow(), 5131 ) 5132 self.local_pred_multi_check_if_list_is_empty() 5133 self._view.ui.btn_pred_multi_prot_seq_overview_remove.setEnabled(False)
Removes the entered sequence to the list of sequences of the protein.
def
local_pred_multi_check_if_list_is_empty(self) -> None:
5135 def local_pred_multi_check_if_list_is_empty(self) -> None: 5136 """Checks if the list of sequences of the protein is empty.""" 5137 if self._view.ui.list_pred_multi_prot_seq_overview.count() == 0: 5138 self._view.ui.btn_pred_multi_prot_to_predict_add_2.setEnabled(False) 5139 else: 5140 self._view.ui.btn_pred_multi_prot_to_predict_add_2.setEnabled(True)
Checks if the list of sequences of the protein is empty.
def
local_pred_multi_add(self) -> None:
5142 def local_pred_multi_add(self) -> None: 5143 """Shows the gui elements for the protein name.""" 5144 gui_elements_to_show = [ 5145 self._view.ui.lbl_pred_multi_prot_to_predict, 5146 self._view.ui.table_pred_multi_prot_to_predict, 5147 self._view.ui.lbl_pred_multi_prot_name, 5148 self._view.ui.txt_pred_multi_prot_name, 5149 self._view.ui.lbl_pred_multi_prot_name_status, 5150 self._view.ui.btn_pred_multi_back, 5151 self._view.ui.btn_pred_multi_next, 5152 ] 5153 gui_elements_to_hide = [ 5154 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5155 self._view.ui.btn_pred_multi_prot_to_predict_add, 5156 self._view.ui.lbl_pred_multi_prot_seq, 5157 self._view.ui.txt_pred_multi_prot_seq, 5158 self._view.ui.lbl_pred_multi_prot_seq_status, 5159 self._view.ui.lbl_pred_multi_prot_seq_add, 5160 self._view.ui.btn_pred_multi_prot_seq_add, 5161 self._view.ui.lbl_pred_multi_prot_seq_overview, 5162 self._view.ui.list_pred_multi_prot_seq_overview, 5163 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5164 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5165 self._view.ui.btn_pred_multi_back_2, 5166 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5167 self._view.ui.lbl_pred_multi_advanced_config, 5168 self._view.ui.btn_pred_multi_advanced_config, 5169 self._view.ui.btn_pred_multi_predict, 5170 ] 5171 gui_utils.show_gui_elements(gui_elements_to_show) 5172 gui_utils.hide_gui_elements(gui_elements_to_hide) 5173 gui_utils.enable_text_box(self._view.ui.txt_pred_multi_prot_name, self._view.ui.lbl_pred_multi_prot_name) 5174 gui_utils.disable_text_box(self._view.ui.txt_pred_multi_prot_seq, self._view.ui.lbl_pred_multi_prot_seq) 5175 self._view.ui.btn_pred_multi_next.setEnabled(False) 5176 self._view.ui.txt_pred_multi_prot_name.clear() 5177 styles.color_button_not_ready(self._view.ui.btn_pred_multi_next) 5178 if self._view.ui.table_pred_multi_prot_to_predict.rowCount() > 0: 5179 try: 5180 self._view.ui.table_pred_multi_prot_to_predict.currentItem().setSelected(False) 5181 except AttributeError: 5182 constants.PYSSA_LOGGER.debug("No selection on Local Multimer Prediction in overview table.")
Shows the gui elements for the protein name.
def
local_pred_multi_back(self) -> None:
5184 def local_pred_multi_back(self) -> None: 5185 """Hides the gui elements for the protein name.""" 5186 gui_elements_to_show = [ 5187 self._view.ui.lbl_pred_multi_prot_to_predict, 5188 self._view.ui.table_pred_multi_prot_to_predict, 5189 self._view.ui.btn_pred_multi_prot_to_predict_add, 5190 ] 5191 gui_elements_to_hide = [ 5192 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5193 self._view.ui.lbl_pred_multi_prot_name, 5194 self._view.ui.txt_pred_multi_prot_name, 5195 self._view.ui.lbl_pred_multi_prot_name_status, 5196 self._view.ui.btn_pred_multi_back, 5197 self._view.ui.btn_pred_multi_next, 5198 self._view.ui.lbl_pred_multi_prot_seq, 5199 self._view.ui.txt_pred_multi_prot_seq, 5200 self._view.ui.lbl_pred_multi_prot_seq_status, 5201 self._view.ui.lbl_pred_multi_prot_seq_add, 5202 self._view.ui.btn_pred_multi_prot_seq_add, 5203 self._view.ui.lbl_pred_multi_prot_seq_overview, 5204 self._view.ui.list_pred_multi_prot_seq_overview, 5205 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5206 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5207 self._view.ui.btn_pred_multi_back_2, 5208 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5209 self._view.ui.lbl_pred_multi_advanced_config, 5210 self._view.ui.btn_pred_multi_advanced_config, 5211 self._view.ui.btn_pred_multi_predict, 5212 ] 5213 gui_utils.show_gui_elements(gui_elements_to_show) 5214 gui_utils.hide_gui_elements(gui_elements_to_hide) 5215 self.local_pred_multi_check_if_table_is_empty()
Hides the gui elements for the protein name.
def
local_pred_multi_next(self) -> None:
5217 def local_pred_multi_next(self) -> None: 5218 """Shows the gui elements for the protein sequence.""" 5219 gui_elements_to_show = [ 5220 self._view.ui.lbl_pred_multi_prot_to_predict, 5221 self._view.ui.table_pred_multi_prot_to_predict, 5222 self._view.ui.lbl_pred_multi_prot_name, 5223 self._view.ui.txt_pred_multi_prot_name, 5224 self._view.ui.lbl_pred_multi_prot_seq, 5225 self._view.ui.txt_pred_multi_prot_seq, 5226 self._view.ui.lbl_pred_multi_prot_seq_status, 5227 self._view.ui.lbl_pred_multi_prot_seq_add, 5228 self._view.ui.btn_pred_multi_prot_seq_add, 5229 self._view.ui.lbl_pred_multi_prot_seq_overview, 5230 self._view.ui.list_pred_multi_prot_seq_overview, 5231 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5232 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5233 self._view.ui.btn_pred_multi_back_2, 5234 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5235 ] 5236 gui_elements_to_hide = [ 5237 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5238 self._view.ui.btn_pred_multi_prot_to_predict_add, 5239 self._view.ui.lbl_pred_multi_prot_name_status, 5240 self._view.ui.btn_pred_multi_back, 5241 self._view.ui.btn_pred_multi_next, 5242 self._view.ui.lbl_pred_multi_advanced_config, 5243 self._view.ui.btn_pred_multi_advanced_config, 5244 self._view.ui.btn_pred_multi_predict, 5245 ] 5246 gui_utils.show_gui_elements(gui_elements_to_show) 5247 gui_utils.hide_gui_elements(gui_elements_to_hide) 5248 gui_utils.enable_text_box(self._view.ui.txt_pred_multi_prot_seq, self._view.ui.lbl_pred_multi_prot_seq) 5249 gui_utils.disable_text_box(self._view.ui.txt_pred_multi_prot_name, self._view.ui.lbl_pred_multi_prot_name) 5250 self._view.ui.txt_pred_multi_prot_seq.clear() 5251 self._view.ui.list_pred_multi_prot_seq_overview.clear() 5252 self._view.ui.btn_pred_multi_prot_to_predict_add_2.setEnabled(False) 5253 self._view.ui.btn_pred_multi_prot_seq_overview_remove.setEnabled(False) 5254 styles.color_button_not_ready(self._view.ui.btn_pred_multi_prot_to_predict_add_2)
Shows the gui elements for the protein sequence.
def
local_pred_multi_back_2(self) -> None:
5256 def local_pred_multi_back_2(self) -> None: 5257 """Hides the gui elements for the protein sequence.""" 5258 gui_elements_to_show = [ 5259 self._view.ui.lbl_pred_multi_prot_to_predict, 5260 self._view.ui.table_pred_multi_prot_to_predict, 5261 self._view.ui.lbl_pred_multi_prot_name_status, 5262 self._view.ui.btn_pred_multi_back, 5263 self._view.ui.btn_pred_multi_next, 5264 self._view.ui.lbl_pred_multi_prot_name, 5265 self._view.ui.txt_pred_multi_prot_name, 5266 ] 5267 gui_elements_to_hide = [ 5268 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5269 self._view.ui.btn_pred_multi_prot_to_predict_add, 5270 self._view.ui.lbl_pred_multi_prot_seq, 5271 self._view.ui.txt_pred_multi_prot_seq, 5272 self._view.ui.lbl_pred_multi_prot_seq_status, 5273 self._view.ui.lbl_pred_multi_prot_seq_add, 5274 self._view.ui.btn_pred_multi_prot_seq_add, 5275 self._view.ui.lbl_pred_multi_prot_seq_overview, 5276 self._view.ui.list_pred_multi_prot_seq_overview, 5277 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5278 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5279 self._view.ui.btn_pred_multi_back_2, 5280 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5281 self._view.ui.lbl_pred_multi_advanced_config, 5282 self._view.ui.btn_pred_multi_advanced_config, 5283 self._view.ui.btn_pred_multi_predict, 5284 ] 5285 gui_utils.show_gui_elements(gui_elements_to_show) 5286 gui_utils.hide_gui_elements(gui_elements_to_hide) 5287 gui_utils.enable_text_box(self._view.ui.txt_pred_multi_prot_name, self._view.ui.lbl_pred_multi_prot_name) 5288 gui_utils.disable_text_box(self._view.ui.txt_pred_multi_prot_seq, self._view.ui.lbl_pred_multi_prot_seq)
Hides the gui elements for the protein sequence.
def
local_pred_multi_prot_seq_overview_item_changed(self) -> None:
5290 def local_pred_multi_prot_seq_overview_item_changed(self) -> None: 5291 """Enables the remove button of the list sequences of the protein.""" 5292 self._view.ui.btn_pred_multi_prot_seq_overview_remove.setEnabled(True)
Enables the remove button of the list sequences of the protein.
def
local_pred_multi_prot_to_predict_item_changed(self) -> None:
5294 def local_pred_multi_prot_to_predict_item_changed(self) -> None: 5295 """Enables the remove button of the table proteins to predict.""" 5296 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(True)
Enables the remove button of the table proteins to predict.
def
local_pred_multi_prot_to_predict_add_2(self) -> None:
5298 def local_pred_multi_prot_to_predict_add_2(self) -> None: 5299 """Adds the protein to the list of proteins to predict.""" 5300 for i in range(self._view.ui.list_pred_multi_prot_seq_overview.count()): 5301 self._view.ui.table_pred_multi_prot_to_predict.setRowCount( 5302 self._view.ui.table_pred_multi_prot_to_predict.rowCount() + 1, 5303 ) 5304 self._view.ui.table_pred_multi_prot_to_predict.insertRow( 5305 self._view.ui.table_pred_multi_prot_to_predict.rowCount() + 1, 5306 ) 5307 tmp_chain_seq = ( 5308 constants.chain_dict.get(i), 5309 self._view.ui.list_pred_multi_prot_seq_overview.item(i).text(), 5310 ) 5311 self._view.ui.table_pred_multi_prot_to_predict.setItem( 5312 self._view.ui.table_pred_multi_prot_to_predict.rowCount() - 1, 5313 0, 5314 QtWidgets.QTableWidgetItem(tmp_chain_seq[0]), 5315 ) 5316 self._view.ui.table_pred_multi_prot_to_predict.setItem( 5317 self._view.ui.table_pred_multi_prot_to_predict.rowCount() - 1, 5318 1, 5319 QtWidgets.QTableWidgetItem(tmp_chain_seq[1]), 5320 ) 5321 name_item = QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_multi_prot_name.text()) 5322 self._view.ui.table_pred_multi_prot_to_predict.setVerticalHeaderItem( 5323 self._view.ui.table_pred_multi_prot_to_predict.rowCount() - 1, 5324 name_item, 5325 ) 5326 self._view.ui.table_pred_multi_prot_to_predict.resizeColumnsToContents() 5327 self.local_pred_multi_check_if_table_is_empty() 5328 gui_elements_to_show = [ 5329 self._view.ui.lbl_pred_multi_prot_to_predict, 5330 self._view.ui.table_pred_multi_prot_to_predict, 5331 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5332 self._view.ui.btn_pred_multi_prot_to_predict_add, 5333 self._view.ui.lbl_pred_multi_advanced_config, 5334 self._view.ui.btn_pred_multi_advanced_config, 5335 self._view.ui.btn_pred_multi_predict, 5336 ] 5337 gui_elements_to_hide = [ 5338 self._view.ui.lbl_pred_multi_prot_name_status, 5339 self._view.ui.btn_pred_multi_back, 5340 self._view.ui.btn_pred_multi_next, 5341 self._view.ui.lbl_pred_multi_prot_name, 5342 self._view.ui.txt_pred_multi_prot_name, 5343 self._view.ui.lbl_pred_multi_prot_seq, 5344 self._view.ui.txt_pred_multi_prot_seq, 5345 self._view.ui.lbl_pred_multi_prot_seq_status, 5346 self._view.ui.lbl_pred_multi_prot_seq_add, 5347 self._view.ui.btn_pred_multi_prot_seq_add, 5348 self._view.ui.lbl_pred_multi_prot_seq_overview, 5349 self._view.ui.list_pred_multi_prot_seq_overview, 5350 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5351 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5352 self._view.ui.btn_pred_multi_back_2, 5353 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5354 ] 5355 gui_utils.show_gui_elements(gui_elements_to_show) 5356 gui_utils.hide_gui_elements(gui_elements_to_hide) 5357 self._init_local_pred_multi_page() 5358 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False)
Adds the protein to the list of proteins to predict.
def
local_pred_multi_remove(self) -> None:
5360 def local_pred_multi_remove(self) -> None: 5361 """Removes the selected protein from the list of proteins to predict.""" 5362 self._view.ui.table_pred_multi_prot_to_predict.removeRow( 5363 self._view.ui.table_pred_multi_prot_to_predict.currentRow(), 5364 ) 5365 if self._view.ui.table_pred_multi_prot_to_predict.rowCount() > 0: 5366 prot_name = self._view.ui.table_pred_multi_prot_to_predict.verticalHeaderItem( 5367 self._view.ui.table_pred_multi_prot_to_predict.currentRow(), 5368 ).text() 5369 for i in range(self._view.ui.table_pred_multi_prot_to_predict.rowCount()): 5370 if self._view.ui.table_pred_multi_prot_to_predict.verticalHeaderItem(i).text() == prot_name: 5371 self._view.ui.table_pred_multi_prot_to_predict.setItem( 5372 i, 5373 0, 5374 QtWidgets.QTableWidgetItem(constants.chain_dict.get(i)), 5375 ) 5376 self.local_pred_multi_check_if_table_is_empty() 5377 gui_elements_to_show = [ 5378 self._view.ui.lbl_pred_multi_prot_to_predict, 5379 self._view.ui.table_pred_multi_prot_to_predict, 5380 self._view.ui.btn_pred_multi_prot_to_predict_remove, 5381 self._view.ui.btn_pred_multi_prot_to_predict_add, 5382 self._view.ui.lbl_pred_multi_advanced_config, 5383 self._view.ui.btn_pred_multi_advanced_config, 5384 self._view.ui.btn_pred_multi_predict, 5385 ] 5386 gui_elements_to_hide = [ 5387 self._view.ui.lbl_pred_multi_prot_name_status, 5388 self._view.ui.btn_pred_multi_back, 5389 self._view.ui.btn_pred_multi_next, 5390 self._view.ui.lbl_pred_multi_prot_name, 5391 self._view.ui.txt_pred_multi_prot_name, 5392 self._view.ui.lbl_pred_multi_prot_seq, 5393 self._view.ui.txt_pred_multi_prot_seq, 5394 self._view.ui.lbl_pred_multi_prot_seq_status, 5395 self._view.ui.lbl_pred_multi_prot_seq_add, 5396 self._view.ui.btn_pred_multi_prot_seq_add, 5397 self._view.ui.lbl_pred_multi_prot_seq_overview, 5398 self._view.ui.list_pred_multi_prot_seq_overview, 5399 self._view.ui.btn_pred_multi_prot_seq_overview_remove, 5400 self._view.ui.lbl_pred_multi_prot_to_predict_2, 5401 self._view.ui.btn_pred_multi_back_2, 5402 self._view.ui.btn_pred_multi_prot_to_predict_add_2, 5403 ] 5404 gui_utils.show_gui_elements(gui_elements_to_show) 5405 gui_utils.hide_gui_elements(gui_elements_to_hide) 5406 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False) 5407 self.local_pred_multi_check_if_table_is_empty()
Removes the selected protein from the list of proteins to predict.
def
display_monomer_pred_analysis(self) -> None:
5433 def display_monomer_pred_analysis(self) -> None: 5434 """Displays the monomer prediction + analysis page.""" 5435 # checks internet connection 5436 if not tools.check_internet_connectivity(): 5437 gui_utils.no_internet_dialog() 5438 return 5439 5440 self._init_mono_pred_analysis_page() 5441 self._view.ui.table_pred_analysis_mono_prot_to_predict.clear() 5442 self._view.ui.table_pred_analysis_mono_prot_to_predict.setHorizontalHeaderItem( 5443 0, 5444 QtWidgets.QTableWidgetItem("Chain"), 5445 ) 5446 self._view.ui.table_pred_analysis_mono_prot_to_predict.setHorizontalHeaderItem( 5447 1, 5448 QtWidgets.QTableWidgetItem("Sequence"), 5449 ) 5450 self._view.ui.table_pred_analysis_mono_prot_to_predict.resizeColumnsToContents() 5451 gui_elements_to_show = [ 5452 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5453 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5454 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5455 ] 5456 gui_elements_to_hide = [ 5457 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5458 self._view.ui.lbl_pred_analysis_mono_prot_name, 5459 self._view.ui.txt_pred_analysis_mono_prot_name, 5460 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5461 self._view.ui.btn_pred_analysis_mono_back, 5462 self._view.ui.btn_pred_analysis_mono_next, 5463 self._view.ui.lbl_pred_analysis_mono_seq_name, 5464 self._view.ui.txt_pred_analysis_mono_seq_name, 5465 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5466 self._view.ui.btn_pred_analysis_mono_back_2, 5467 self._view.ui.btn_pred_analysis_mono_add_protein, 5468 self._view.ui.lbl_pred_mono_advanced_config_2, 5469 self._view.ui.btn_pred_mono_advanced_config_2, 5470 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5471 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5472 ] 5473 gui_utils.show_gui_elements(gui_elements_to_show) 5474 gui_utils.hide_gui_elements(gui_elements_to_hide) 5475 if self._view.ui.tabWidget.currentIndex() == 1: 5476 self._view.ui.tabWidget.setCurrentIndex(0) 5477 self._view.ui.tabWidget.setTabEnabled(1, False) 5478 self._view.ui.tabWidget.setTabEnabled(0, True) 5479 tools.switch_page( 5480 self._view.ui.stackedWidget, 5481 self._view.ui.lbl_page_title, 5482 21, 5483 "Monomer Prediction + Analysis", 5484 ) 5485 self.last_sidebar_button = styles.color_sidebar_buttons( 5486 self.last_sidebar_button, 5487 self._view.ui.btn_pred_analysis_monomer_page, 5488 ) 5489 self._view.ui.table_pred_analysis_mono_prot_to_predict.setEnabled(True)
Displays the monomer prediction + analysis page.
def
mono_pred_analysis_validate_protein_name(self) -> None:
5494 def mono_pred_analysis_validate_protein_name(self) -> None: 5495 """Validates the input of the protein name in real-time.""" 5496 if safeguard.Safeguard.check_if_value_is_in_table_v_header( 5497 self._view.ui.txt_pred_analysis_mono_prot_name.text(), 5498 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5499 ): 5500 self._view.ui.lbl_pred_analysis_mono_prot_name_status.setText("Protein name already used.") 5501 self._view.ui.btn_pred_analysis_mono_next.setEnabled(False) 5502 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_mono_next) 5503 else: 5504 self._view.ui.btn_pred_analysis_mono_next.setEnabled(True) 5505 tools.validate_protein_name( 5506 self._view.ui.txt_pred_analysis_mono_prot_name, 5507 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5508 self._view.ui.btn_pred_analysis_mono_next, 5509 )
Validates the input of the protein name in real-time.
def
mono_pred_analysis_validate_protein_sequence(self) -> None:
5511 def mono_pred_analysis_validate_protein_sequence(self) -> None: 5512 """Validates the input of the protein sequence in real-time.""" 5513 tools.validate_protein_sequence( 5514 self._view.ui.txt_pred_analysis_mono_seq_name, 5515 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5516 self._view.ui.btn_pred_analysis_mono_add_protein, 5517 )
Validates the input of the protein sequence in real-time.
def
mono_pred_analysis_check_if_table_is_empty(self) -> None:
5519 def mono_pred_analysis_check_if_table_is_empty(self) -> None: 5520 """Checks if the table proteins to predict is empty.""" 5521 if self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() == 0: 5522 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_mono_go_analysis_setup) 5523 self._view.ui.btn_pred_analysis_mono_go_analysis_setup.setEnabled(False) 5524 gui_elements_to_show = [ 5525 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5526 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5527 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5528 ] 5529 gui_elements_to_hide = [ 5530 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5531 self._view.ui.lbl_pred_analysis_mono_prot_name, 5532 self._view.ui.txt_pred_analysis_mono_prot_name, 5533 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5534 self._view.ui.btn_pred_analysis_mono_back, 5535 self._view.ui.btn_pred_analysis_mono_next, 5536 self._view.ui.lbl_pred_analysis_mono_seq_name, 5537 self._view.ui.txt_pred_analysis_mono_seq_name, 5538 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5539 self._view.ui.btn_pred_analysis_mono_back_2, 5540 self._view.ui.btn_pred_analysis_mono_add_protein, 5541 self._view.ui.lbl_pred_mono_advanced_config_2, 5542 self._view.ui.btn_pred_mono_advanced_config_2, 5543 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5544 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5545 ] 5546 gui_utils.show_gui_elements(gui_elements_to_show) 5547 gui_utils.hide_gui_elements(gui_elements_to_hide) 5548 else: 5549 gui_elements_to_show = [ 5550 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5551 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5552 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5553 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5554 self._view.ui.lbl_pred_mono_advanced_config_2, 5555 self._view.ui.btn_pred_mono_advanced_config_2, 5556 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5557 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5558 ] 5559 gui_elements_to_hide = [ 5560 self._view.ui.lbl_pred_analysis_mono_prot_name, 5561 self._view.ui.txt_pred_analysis_mono_prot_name, 5562 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5563 self._view.ui.btn_pred_analysis_mono_back, 5564 self._view.ui.btn_pred_analysis_mono_next, 5565 self._view.ui.lbl_pred_analysis_mono_seq_name, 5566 self._view.ui.txt_pred_analysis_mono_seq_name, 5567 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5568 self._view.ui.btn_pred_analysis_mono_back_2, 5569 self._view.ui.btn_pred_analysis_mono_add_protein, 5570 ] 5571 gui_utils.show_gui_elements(gui_elements_to_show) 5572 gui_utils.hide_gui_elements(gui_elements_to_hide) 5573 self._view.ui.btn_pred_analysis_mono_go_analysis_setup.setEnabled(True)
Checks if the table proteins to predict is empty.
def
setup_defaults_monomer_prediction_analysis(self) -> None:
5575 def setup_defaults_monomer_prediction_analysis(self) -> None: 5576 """Sets up default values for the prediction tab.""" 5577 # clears everything 5578 self._view.ui.txt_pred_analysis_mono_prot_name.clear() 5579 self._view.ui.txt_pred_analysis_mono_seq_name.clear() 5580 # sets up defaults: Prediction 5581 self._view.ui.btn_pred_analysis_mono_next.setEnabled(False) 5582 self._view.ui.btn_pred_analysis_mono_add_protein.setEnabled(False) 5583 self._view.ui.lbl_pred_analysis_mono_prot_name_status.setText("") 5584 self._view.ui.lbl_pred_analysis_mono_seq_name_status.setText("")
Sets up default values for the prediction tab.
def
mono_pred_analysis_add_seq_to_predict(self) -> None:
5586 def mono_pred_analysis_add_seq_to_predict(self) -> None: 5587 """Shows the gui elements for the protein name.""" 5588 gui_elements_to_show = [ 5589 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5590 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5591 self._view.ui.lbl_pred_analysis_mono_prot_name, 5592 self._view.ui.txt_pred_analysis_mono_prot_name, 5593 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5594 self._view.ui.btn_pred_analysis_mono_back, 5595 self._view.ui.btn_pred_analysis_mono_next, 5596 ] 5597 gui_utils.enable_text_box( 5598 self._view.ui.txt_pred_analysis_mono_prot_name, 5599 self._view.ui.lbl_pred_analysis_mono_prot_name, 5600 ) 5601 gui_elements_to_hide = [ 5602 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5603 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5604 self._view.ui.lbl_pred_analysis_mono_seq_name, 5605 self._view.ui.txt_pred_analysis_mono_seq_name, 5606 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5607 self._view.ui.btn_pred_analysis_mono_back_2, 5608 self._view.ui.btn_pred_analysis_mono_add_protein, 5609 self._view.ui.lbl_pred_mono_advanced_config_2, 5610 self._view.ui.btn_pred_mono_advanced_config_2, 5611 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5612 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5613 ] 5614 gui_utils.disable_text_box( 5615 self._view.ui.txt_pred_analysis_mono_seq_name, 5616 self._view.ui.lbl_pred_analysis_mono_seq_name, 5617 ) 5618 gui_utils.show_gui_elements(gui_elements_to_show) 5619 gui_utils.hide_gui_elements(gui_elements_to_hide) 5620 self._view.ui.btn_pred_analysis_mono_next.setEnabled(False) 5621 self._view.ui.txt_pred_analysis_mono_prot_name.clear() 5622 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_mono_next) 5623 if self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() > 0: 5624 try: 5625 self._view.ui.table_pred_analysis_mono_prot_to_predict.currentItem().setSelected(False) 5626 except AttributeError: 5627 constants.PYSSA_LOGGER.debug("No selection on Local Monomer Prediction in overview table.")
Shows the gui elements for the protein name.
def
mono_pred_analysis_back(self) -> None:
5629 def mono_pred_analysis_back(self) -> None: 5630 """Hides the gui elements for the protein name.""" 5631 gui_elements_to_show = [ 5632 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5633 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5634 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5635 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5636 ] 5637 gui_elements_to_hide = [ 5638 self._view.ui.lbl_pred_analysis_mono_prot_name, 5639 self._view.ui.txt_pred_analysis_mono_prot_name, 5640 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5641 self._view.ui.btn_pred_analysis_mono_back, 5642 self._view.ui.btn_pred_analysis_mono_next, 5643 self._view.ui.lbl_pred_analysis_mono_seq_name, 5644 self._view.ui.txt_pred_analysis_mono_seq_name, 5645 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5646 self._view.ui.btn_pred_analysis_mono_back_2, 5647 self._view.ui.btn_pred_analysis_mono_add_protein, 5648 self._view.ui.lbl_pred_mono_advanced_config_2, 5649 self._view.ui.btn_pred_mono_advanced_config_2, 5650 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5651 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5652 ] 5653 gui_utils.show_gui_elements(gui_elements_to_show) 5654 gui_utils.hide_gui_elements(gui_elements_to_hide) 5655 self.mono_pred_analysis_check_if_table_is_empty() 5656 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.setEnabled(False)
Hides the gui elements for the protein name.
def
mono_pred_analysis_next(self) -> None:
5658 def mono_pred_analysis_next(self) -> None: 5659 """Shows the gui elements for the protein sequence.""" 5660 gui_elements_to_show = [ 5661 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5662 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5663 self._view.ui.lbl_pred_analysis_mono_prot_name, 5664 self._view.ui.txt_pred_analysis_mono_prot_name, 5665 self._view.ui.lbl_pred_analysis_mono_seq_name, 5666 self._view.ui.txt_pred_analysis_mono_seq_name, 5667 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5668 self._view.ui.btn_pred_analysis_mono_back_2, 5669 self._view.ui.btn_pred_analysis_mono_add_protein, 5670 ] 5671 gui_utils.enable_text_box( 5672 self._view.ui.txt_pred_analysis_mono_seq_name, 5673 self._view.ui.lbl_pred_analysis_mono_seq_name, 5674 ) 5675 gui_elements_to_hide = [ 5676 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5677 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5678 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5679 self._view.ui.btn_pred_analysis_mono_back, 5680 self._view.ui.btn_pred_analysis_mono_next, 5681 self._view.ui.lbl_pred_mono_advanced_config_2, 5682 self._view.ui.btn_pred_mono_advanced_config_2, 5683 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5684 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5685 ] 5686 gui_utils.disable_text_box( 5687 self._view.ui.txt_pred_analysis_mono_prot_name, 5688 self._view.ui.lbl_pred_analysis_mono_prot_name, 5689 ) 5690 gui_utils.show_gui_elements(gui_elements_to_show) 5691 gui_utils.hide_gui_elements(gui_elements_to_hide) 5692 self._view.ui.txt_pred_analysis_mono_seq_name.clear()
Shows the gui elements for the protein sequence.
def
mono_pred_analysis_back_2(self) -> None:
5694 def mono_pred_analysis_back_2(self) -> None: 5695 """Hides the gui elements for the protein sequence.""" 5696 gui_elements_to_show = [ 5697 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5698 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5699 self._view.ui.lbl_pred_analysis_mono_prot_name, 5700 self._view.ui.txt_pred_analysis_mono_prot_name, 5701 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5702 self._view.ui.btn_pred_analysis_mono_back, 5703 self._view.ui.btn_pred_analysis_mono_next, 5704 ] 5705 gui_elements_to_hide = [ 5706 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5707 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5708 self._view.ui.lbl_pred_analysis_mono_seq_name, 5709 self._view.ui.txt_pred_analysis_mono_seq_name, 5710 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5711 self._view.ui.btn_pred_analysis_mono_back_2, 5712 self._view.ui.btn_pred_analysis_mono_add_protein, 5713 self._view.ui.lbl_pred_mono_advanced_config_2, 5714 self._view.ui.btn_pred_mono_advanced_config_2, 5715 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5716 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5717 ] 5718 gui_utils.enable_text_box( 5719 self._view.ui.txt_pred_analysis_mono_prot_name, 5720 self._view.ui.lbl_pred_analysis_mono_prot_name, 5721 ) 5722 gui_utils.disable_text_box( 5723 self._view.ui.txt_pred_analysis_mono_seq_name, 5724 self._view.ui.lbl_pred_analysis_mono_seq_name, 5725 ) 5726 gui_utils.show_gui_elements(gui_elements_to_show) 5727 gui_utils.hide_gui_elements(gui_elements_to_hide)
Hides the gui elements for the protein sequence.
def
mono_pred_analysis_add_protein(self) -> None:
5729 def mono_pred_analysis_add_protein(self) -> None: 5730 """Adds the protein to the list of proteins to predict.""" 5731 self._view.ui.table_pred_analysis_mono_prot_to_predict.setRowCount( 5732 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() + 1, 5733 ) 5734 self._view.ui.table_pred_analysis_mono_prot_to_predict.insertRow( 5735 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() + 1, 5736 ) 5737 self._view.ui.table_pred_analysis_mono_prot_to_predict.setItem( 5738 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5739 0, 5740 QtWidgets.QTableWidgetItem("A"), 5741 ) 5742 self._view.ui.table_pred_analysis_mono_prot_to_predict.setItem( 5743 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5744 1, 5745 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_analysis_mono_seq_name.toPlainText()), 5746 ) 5747 self._view.ui.table_pred_analysis_mono_prot_to_predict.setVerticalHeaderItem( 5748 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5749 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_analysis_mono_prot_name.text()), 5750 ) 5751 self._view.ui.table_pred_analysis_mono_prot_to_predict.resizeColumnsToContents() 5752 self.mono_pred_analysis_check_if_table_is_empty() 5753 gui_elements_to_show = [ 5754 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 5755 self._view.ui.table_pred_analysis_mono_prot_to_predict, 5756 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 5757 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 5758 self._view.ui.lbl_pred_mono_advanced_config_2, 5759 self._view.ui.btn_pred_mono_advanced_config_2, 5760 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 5761 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 5762 ] 5763 gui_utils.enable_text_box( 5764 self._view.ui.txt_pred_analysis_mono_prot_name, 5765 self._view.ui.lbl_pred_analysis_mono_prot_name, 5766 ) 5767 gui_elements_to_hide = [ 5768 self._view.ui.lbl_pred_analysis_mono_prot_name, 5769 self._view.ui.txt_pred_analysis_mono_prot_name, 5770 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 5771 self._view.ui.btn_pred_analysis_mono_back, 5772 self._view.ui.btn_pred_analysis_mono_next, 5773 self._view.ui.lbl_pred_analysis_mono_seq_name, 5774 self._view.ui.txt_pred_analysis_mono_seq_name, 5775 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 5776 self._view.ui.btn_pred_analysis_mono_back_2, 5777 self._view.ui.btn_pred_analysis_mono_add_protein, 5778 ] 5779 gui_utils.show_gui_elements(gui_elements_to_show) 5780 gui_utils.hide_gui_elements(gui_elements_to_hide) 5781 self._view.ui.btn_pred_analysis_mono_go_analysis_setup.setEnabled(True) 5782 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.setEnabled(False) 5783 self.setup_defaults_monomer_prediction()
Adds the protein to the list of proteins to predict.
def
mono_pred_analysis_prediction_overview_item_clicked(self) -> None:
5785 def mono_pred_analysis_prediction_overview_item_clicked(self) -> None: 5786 """Enables the remove button.""" 5787 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.setEnabled(True)
Enables the remove button.
def
mono_pred_analysis_add_protein_to_predict(self) -> None:
5789 def mono_pred_analysis_add_protein_to_predict(self) -> None: 5790 """Needs to be removed.""" 5791 self._view.ui.table_pred_analysis_mono_prot_to_predict.setRowCount( 5792 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() + 1, 5793 ) 5794 self._view.ui.table_pred_analysis_mono_prot_to_predict.insertRow( 5795 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() + 1, 5796 ) 5797 self._view.ui.table_pred_analysis_mono_prot_to_predict.setItem( 5798 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5799 0, 5800 QtWidgets.QTableWidgetItem("A"), 5801 ) 5802 self._view.ui.table_pred_analysis_mono_prot_to_predict.setItem( 5803 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5804 1, 5805 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_analysis_mono_seq_name.toPlainText()), 5806 ) 5807 self._view.ui.table_pred_analysis_mono_prot_to_predict.setVerticalHeaderItem( 5808 self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount() - 1, 5809 QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_analysis_mono_prot_name.text()), 5810 ) 5811 self._view.ui.table_pred_analysis_mono_prot_to_predict.resizeColumnsToContents() 5812 self.mono_pred_analysis_check_if_table_is_empty() 5813 self.setup_defaults_monomer_prediction_analysis()
Needs to be removed.
def
mono_pred_analysis_remove_protein_to_predict(self) -> None:
5815 def mono_pred_analysis_remove_protein_to_predict(self) -> None: 5816 """Removes the selected protein from the list of proteins to predict.""" 5817 self._view.ui.table_pred_analysis_mono_prot_to_predict.removeRow( 5818 self._view.ui.table_pred_analysis_mono_prot_to_predict.currentRow(), 5819 ) 5820 self.mono_pred_analysis_check_if_table_is_empty() 5821 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.setEnabled(False)
Removes the selected protein from the list of proteins to predict.
def
mono_pred_analysis_structure_analysis_add(self) -> None:
5826 def mono_pred_analysis_structure_analysis_add(self) -> None: 5827 """Shows the gui elements for the selection of the two proteins.""" 5828 gui_elements_to_show = [ 5829 self._view.ui.lbl_pred_analysis_mono_overview, 5830 self._view.ui.list_pred_analysis_mono_overview, 5831 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 5832 self._view.ui.box_pred_analysis_mono_prot_struct_1, 5833 self._view.ui.lbl_analysis_batch_vs_2, 5834 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 5835 self._view.ui.box_pred_analysis_mono_prot_struct_2, 5836 self._view.ui.btn_pred_analysis_mono_back_3, 5837 self._view.ui.btn_pred_analysis_mono_next_2, 5838 ] 5839 gui_elements_to_hide = [ 5840 self._view.ui.btn_pred_analysis_mono_remove, 5841 self._view.ui.btn_pred_analysis_mono_add, 5842 self._view.ui.lbl_pred_analysis_mono_ref_chains, 5843 self._view.ui.list_pred_analysis_mono_ref_chains, 5844 self._view.ui.btn_pred_analysis_mono_back_4, 5845 self._view.ui.btn_pred_analysis_mono_next_3, 5846 self._view.ui.lbl_pred_analysis_mono_model_chains, 5847 self._view.ui.list_pred_analysis_mono_model_chains, 5848 self._view.ui.btn_pred_analysis_mono_back_5, 5849 self._view.ui.btn_pred_analysis_mono_next_4, 5850 self._view.ui.lbl_pred_analysis_mono_images, 5851 self._view.ui.cb_pred_analysis_mono_images, 5852 self._view.ui.btn_pred_analysis_mono_start, 5853 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 5854 ] 5855 gui_utils.show_gui_elements(gui_elements_to_show) 5856 gui_utils.hide_gui_elements(gui_elements_to_hide) 5857 self._view.ui.lbl_pred_analysis_mono_prot_struct_1.clear() 5858 self._view.ui.lbl_pred_analysis_mono_prot_struct_2.clear() 5859 self._view.ui.lbl_pred_analysis_mono_prot_struct_1.setText("Protein structure 1") 5860 self._view.ui.lbl_pred_analysis_mono_prot_struct_2.setText("Protein structure 2") 5861 self.fill_mono_pred_analysis_protein_boxes() 5862 if self._view.ui.list_pred_analysis_mono_overview.count() > 0: 5863 try: 5864 self._view.ui.list_pred_analysis_mono_overview.currentItem().setSelected(False) 5865 except AttributeError: 5866 constants.PYSSA_LOGGER.debug("No selection in struction analysis overview.")
Shows the gui elements for the selection of the two proteins.
def
mono_pred_analysis_structure_analysis_back_3(self) -> None:
5868 def mono_pred_analysis_structure_analysis_back_3(self) -> None: 5869 """Hides the gui elements to select the two proteins.""" 5870 gui_elements_to_show = [ 5871 self._view.ui.lbl_pred_analysis_mono_overview, 5872 self._view.ui.list_pred_analysis_mono_overview, 5873 self._view.ui.btn_pred_analysis_mono_add, 5874 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 5875 ] 5876 gui_elements_to_hide = [ 5877 self._view.ui.btn_pred_analysis_mono_remove, 5878 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 5879 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 5880 self._view.ui.lbl_analysis_batch_vs_2, 5881 self._view.ui.lbl_pred_analysis_mono_ref_chains, 5882 self._view.ui.list_pred_analysis_mono_ref_chains, 5883 self._view.ui.btn_pred_analysis_mono_back_4, 5884 self._view.ui.btn_pred_analysis_mono_next_3, 5885 self._view.ui.box_pred_analysis_mono_prot_struct_1, 5886 self._view.ui.box_pred_analysis_mono_prot_struct_2, 5887 self._view.ui.btn_pred_analysis_mono_back_3, 5888 self._view.ui.btn_pred_analysis_mono_next_2, 5889 self._view.ui.lbl_pred_analysis_mono_model_chains, 5890 self._view.ui.list_pred_analysis_mono_model_chains, 5891 self._view.ui.btn_pred_analysis_mono_back_5, 5892 self._view.ui.btn_pred_analysis_mono_next_4, 5893 self._view.ui.lbl_pred_analysis_mono_images, 5894 self._view.ui.cb_pred_analysis_mono_images, 5895 self._view.ui.btn_pred_analysis_mono_start, 5896 ] 5897 gui_utils.show_gui_elements(gui_elements_to_show) 5898 gui_utils.hide_gui_elements(gui_elements_to_hide) 5899 if self._view.ui.list_pred_analysis_mono_overview.count() > 0: 5900 self._view.ui.btn_pred_analysis_mono_remove.show() 5901 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(False) 5902 self._view.ui.btn_pred_analysis_mono_start.show() 5903 self._view.ui.lbl_pred_analysis_mono_images.show() 5904 self._view.ui.cb_pred_analysis_mono_images.show()
Hides the gui elements to select the two proteins.
def
mono_pred_analysis_structure_analysis_next_3(self) -> None:
5906 def mono_pred_analysis_structure_analysis_next_3(self) -> None: 5907 """Shows the gui elements to select the chains of protein 2.""" 5908 gui_elements_to_show = [ 5909 self._view.ui.lbl_pred_analysis_mono_overview, 5910 self._view.ui.list_pred_analysis_mono_overview, 5911 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 5912 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 5913 self._view.ui.lbl_analysis_batch_vs_2, 5914 self._view.ui.lbl_pred_analysis_mono_ref_chains, 5915 self._view.ui.list_pred_analysis_mono_ref_chains, 5916 self._view.ui.lbl_pred_analysis_mono_model_chains, 5917 self._view.ui.list_pred_analysis_mono_model_chains, 5918 self._view.ui.btn_pred_analysis_mono_back_5, 5919 self._view.ui.btn_pred_analysis_mono_next_4, 5920 ] 5921 gui_elements_to_hide = [ 5922 self._view.ui.btn_pred_analysis_mono_remove, 5923 self._view.ui.btn_pred_analysis_mono_add, 5924 self._view.ui.box_pred_analysis_mono_prot_struct_1, 5925 self._view.ui.box_pred_analysis_mono_prot_struct_2, 5926 self._view.ui.btn_pred_analysis_mono_back_3, 5927 self._view.ui.btn_pred_analysis_mono_next_2, 5928 self._view.ui.btn_pred_analysis_mono_back_4, 5929 self._view.ui.btn_pred_analysis_mono_next_3, 5930 self._view.ui.lbl_pred_analysis_mono_images, 5931 self._view.ui.cb_pred_analysis_mono_images, 5932 self._view.ui.btn_pred_analysis_mono_start, 5933 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 5934 ] 5935 gui_utils.show_gui_elements(gui_elements_to_show) 5936 gui_utils.hide_gui_elements(gui_elements_to_hide) 5937 self._view.ui.list_pred_analysis_mono_model_chains.clear() 5938 self._view.ui.list_pred_analysis_mono_ref_chains.setEnabled(False) 5939 self._view.ui.btn_pred_analysis_mono_next_4.setEnabled(False) 5940 5941 for i in range(self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount()): 5942 if ( 5943 self._view.ui.table_pred_analysis_mono_prot_to_predict.verticalHeaderItem(i).text() 5944 == self._view.ui.box_pred_analysis_mono_prot_struct_2.currentText() 5945 ): 5946 self._view.ui.list_pred_analysis_mono_model_chains.addItem( 5947 self._view.ui.table_pred_analysis_mono_prot_to_predict.item(i, 0).text(), 5948 ) 5949 if self._view.ui.list_pred_analysis_mono_model_chains.count() == 0: 5950 tmp_protein = self._current_project.search_protein( 5951 self._view.ui.box_pred_analysis_mono_prot_struct_2.currentText(), 5952 ) 5953 for tmp_chain in tmp_protein.chains: 5954 if tmp_chain.chain_type == "protein_chain": 5955 self._view.ui.list_pred_analysis_mono_model_chains.addItem(tmp_chain.chain_letter) 5956 if self._view.ui.list_pred_analysis_mono_model_chains.count() == 1: 5957 self._view.ui.lbl_pred_analysis_mono_model_chains.setText( 5958 f"Select chain in protein structure {self._view.ui.lbl_pred_analysis_mono_prot_struct_2.text()}.", 5959 ) 5960 else: 5961 self._view.ui.lbl_pred_analysis_mono_model_chains.setText( 5962 f"Select {len(self._view.ui.list_pred_analysis_mono_model_chains.selectedItems())} chains " 5963 f"in protein structure {self._view.ui.lbl_pred_analysis_mono_prot_struct_2.text()}.", 5964 )
Shows the gui elements to select the chains of protein 2.
def
mono_pred_analysis_structure_analysis_back_4(self) -> None:
5966 def mono_pred_analysis_structure_analysis_back_4(self) -> None: 5967 """Hides the gui elements to select the chains in protein 1.""" 5968 gui_elements_to_show = [ 5969 self._view.ui.lbl_pred_analysis_mono_overview, 5970 self._view.ui.list_pred_analysis_mono_overview, 5971 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 5972 self._view.ui.box_pred_analysis_mono_prot_struct_1, 5973 self._view.ui.lbl_analysis_batch_vs_2, 5974 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 5975 self._view.ui.box_pred_analysis_mono_prot_struct_2, 5976 self._view.ui.btn_pred_analysis_mono_back_3, 5977 self._view.ui.btn_pred_analysis_mono_next_2, 5978 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 5979 ] 5980 gui_elements_to_hide = [ 5981 self._view.ui.btn_pred_analysis_mono_remove, 5982 self._view.ui.btn_pred_analysis_mono_add, 5983 self._view.ui.lbl_pred_analysis_mono_ref_chains, 5984 self._view.ui.list_pred_analysis_mono_ref_chains, 5985 self._view.ui.btn_pred_analysis_mono_back_4, 5986 self._view.ui.btn_pred_analysis_mono_next_3, 5987 self._view.ui.lbl_pred_analysis_mono_model_chains, 5988 self._view.ui.list_pred_analysis_mono_model_chains, 5989 self._view.ui.btn_pred_analysis_mono_back_5, 5990 self._view.ui.btn_pred_analysis_mono_next_4, 5991 self._view.ui.lbl_pred_analysis_mono_images, 5992 self._view.ui.cb_pred_analysis_mono_images, 5993 self._view.ui.btn_pred_analysis_mono_start, 5994 ] 5995 gui_utils.show_gui_elements(gui_elements_to_show) 5996 gui_utils.hide_gui_elements(gui_elements_to_hide) 5997 self._view.ui.lbl_pred_analysis_mono_prot_struct_1.setText("Protein structure 1") 5998 self._view.ui.lbl_pred_analysis_mono_prot_struct_2.setText("Protein structure 2")
Hides the gui elements to select the chains in protein 1.
def
mono_pred_analysis_structure_analysis_next_4(self) -> None:
6000 def mono_pred_analysis_structure_analysis_next_4(self) -> None: 6001 """Adds the protein pair to the list of protein pairs to analyze.""" 6002 gui_elements_to_show = [ 6003 self._view.ui.btn_pred_analysis_mono_remove, 6004 self._view.ui.btn_pred_analysis_mono_add, 6005 self._view.ui.lbl_pred_analysis_mono_overview, 6006 self._view.ui.list_pred_analysis_mono_overview, 6007 self._view.ui.lbl_pred_analysis_mono_images, 6008 self._view.ui.cb_pred_analysis_mono_images, 6009 self._view.ui.btn_pred_analysis_mono_start, 6010 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 6011 ] 6012 gui_elements_to_hide = [ 6013 self._view.ui.box_pred_analysis_mono_prot_struct_1, 6014 self._view.ui.box_pred_analysis_mono_prot_struct_2, 6015 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 6016 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 6017 self._view.ui.lbl_analysis_batch_vs_2, 6018 self._view.ui.lbl_pred_analysis_mono_ref_chains, 6019 self._view.ui.list_pred_analysis_mono_ref_chains, 6020 self._view.ui.lbl_pred_analysis_mono_model_chains, 6021 self._view.ui.list_pred_analysis_mono_model_chains, 6022 self._view.ui.btn_pred_analysis_mono_back_3, 6023 self._view.ui.btn_pred_analysis_mono_next_2, 6024 self._view.ui.btn_pred_analysis_mono_back_4, 6025 self._view.ui.btn_pred_analysis_mono_next_3, 6026 self._view.ui.btn_pred_analysis_mono_back_5, 6027 self._view.ui.btn_pred_analysis_mono_next_4, 6028 ] 6029 gui_utils.show_gui_elements(gui_elements_to_show) 6030 gui_utils.hide_gui_elements(gui_elements_to_hide) 6031 prot_1_name = self._view.ui.lbl_pred_analysis_mono_prot_struct_1.text() 6032 prot_1_chains = [] 6033 for chain in self._view.ui.list_pred_analysis_mono_ref_chains.selectedItems(): 6034 prot_1_chains.append(chain.text()) 6035 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 6036 prot_2_name = self._view.ui.lbl_pred_analysis_mono_prot_struct_2.text() 6037 prot_2_chains = [] 6038 for chain in self._view.ui.list_pred_analysis_mono_model_chains.selectedItems(): 6039 prot_2_chains.append(chain.text()) 6040 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 6041 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 6042 item = QtWidgets.QListWidgetItem(analysis_name) 6043 self._view.ui.list_pred_analysis_mono_overview.addItem(item) 6044 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(False)
Adds the protein pair to the list of protein pairs to analyze.
def
mono_pred_analysis_structure_analysis_back_5(self) -> None:
6046 def mono_pred_analysis_structure_analysis_back_5(self) -> None: 6047 """Hides the gui elements to select the chains in protein 2.""" 6048 gui_elements_to_show = [ 6049 self._view.ui.lbl_pred_analysis_mono_overview, 6050 self._view.ui.list_pred_analysis_mono_overview, 6051 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 6052 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 6053 self._view.ui.lbl_analysis_batch_vs_2, 6054 self._view.ui.lbl_pred_analysis_mono_ref_chains, 6055 self._view.ui.list_pred_analysis_mono_ref_chains, 6056 self._view.ui.btn_pred_analysis_mono_back_4, 6057 self._view.ui.btn_pred_analysis_mono_next_3, 6058 ] 6059 gui_elements_to_hide = [ 6060 self._view.ui.btn_pred_analysis_mono_remove, 6061 self._view.ui.btn_pred_analysis_mono_add, 6062 self._view.ui.box_pred_analysis_mono_prot_struct_1, 6063 self._view.ui.box_pred_analysis_mono_prot_struct_2, 6064 self._view.ui.btn_pred_analysis_mono_back_3, 6065 self._view.ui.btn_pred_analysis_mono_next_2, 6066 self._view.ui.btn_pred_analysis_mono_back_5, 6067 self._view.ui.btn_pred_analysis_mono_next_4, 6068 self._view.ui.lbl_pred_analysis_mono_images, 6069 self._view.ui.cb_pred_analysis_mono_images, 6070 self._view.ui.btn_pred_analysis_mono_start, 6071 self._view.ui.lbl_pred_analysis_mono_model_chains, 6072 self._view.ui.list_pred_analysis_mono_model_chains, 6073 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 6074 ] 6075 gui_utils.show_gui_elements(gui_elements_to_show) 6076 gui_utils.hide_gui_elements(gui_elements_to_hide) 6077 self._view.ui.list_pred_analysis_mono_ref_chains.setEnabled(True) 6078 6079 # tmp_protein = self._current_project.search_protein(self._view.ui.box_pred_analysis_mono_prot_struct_2.currentText()) 6080 # for tmp_chain in tmp_protein.chains: 6081 # if tmp_chain.chain_type == "protein_chain": 6082 # self._view.ui.list_pred_analysis_mono_ref_chains.addItem(tmp_chain.chain_letter)
Hides the gui elements to select the chains in protein 2.
def
mono_pred_analysis_structure_analysis_overview_clicked(self) -> None:
6084 def mono_pred_analysis_structure_analysis_overview_clicked(self) -> None: 6085 """Enables the remove button.""" 6086 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(True)
Enables the remove button.
def
fill_mono_pred_analysis_protein_boxes(self) -> None:
6088 def fill_mono_pred_analysis_protein_boxes(self) -> None: 6089 """Fills the combo box of the protein structures.""" 6090 protein_names = [] 6091 for i in range(self._view.ui.table_pred_analysis_mono_prot_to_predict.rowCount()): 6092 protein_names.append(self._view.ui.table_pred_analysis_mono_prot_to_predict.verticalHeaderItem(i).text()) 6093 for tmp_protein in self._current_project.proteins: 6094 protein_names.append(tmp_protein.get_molecule_object()) 6095 protein_names.insert(0, "") 6096 self._view.ui.box_pred_analysis_mono_prot_struct_1.clear() 6097 self._view.ui.box_pred_analysis_mono_prot_struct_2.clear() 6098 gui_utils.fill_combo_box(self._view.ui.box_pred_analysis_mono_prot_struct_1, protein_names) 6099 gui_utils.fill_combo_box(self._view.ui.box_pred_analysis_mono_prot_struct_2, protein_names)
Fills the combo box of the protein structures.
def
remove_mono_pred_analysis_analysis_run(self) -> None:
6101 def remove_mono_pred_analysis_analysis_run(self) -> None: 6102 """Removes a selected protein pair form the list of protein pairs to analyze.""" 6103 self._view.ui.list_pred_analysis_mono_overview.takeItem( 6104 self._view.ui.list_pred_analysis_mono_overview.currentRow(), 6105 ) 6106 gui_elements_to_show = [ 6107 self._view.ui.lbl_pred_analysis_mono_overview, 6108 self._view.ui.list_pred_analysis_mono_overview, 6109 self._view.ui.btn_pred_analysis_mono_add, 6110 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 6111 ] 6112 gui_elements_to_hide = [ 6113 self._view.ui.btn_pred_analysis_mono_remove, 6114 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 6115 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 6116 self._view.ui.lbl_analysis_batch_vs_2, 6117 self._view.ui.lbl_pred_analysis_mono_ref_chains, 6118 self._view.ui.list_pred_analysis_mono_ref_chains, 6119 self._view.ui.btn_pred_analysis_mono_back_4, 6120 self._view.ui.btn_pred_analysis_mono_next_3, 6121 self._view.ui.box_pred_analysis_mono_prot_struct_1, 6122 self._view.ui.box_pred_analysis_mono_prot_struct_2, 6123 self._view.ui.btn_pred_analysis_mono_back_3, 6124 self._view.ui.btn_pred_analysis_mono_next_2, 6125 self._view.ui.lbl_pred_analysis_mono_model_chains, 6126 self._view.ui.list_pred_analysis_mono_model_chains, 6127 self._view.ui.btn_pred_analysis_mono_back_5, 6128 self._view.ui.btn_pred_analysis_mono_next_4, 6129 self._view.ui.lbl_pred_analysis_mono_images, 6130 self._view.ui.cb_pred_analysis_mono_images, 6131 self._view.ui.btn_pred_analysis_mono_start, 6132 ] 6133 gui_utils.show_gui_elements(gui_elements_to_show) 6134 gui_utils.hide_gui_elements(gui_elements_to_hide) 6135 if self._view.ui.list_pred_analysis_mono_overview.count() > 0: 6136 self._view.ui.btn_pred_analysis_mono_remove.show() 6137 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(False) 6138 self._view.ui.btn_pred_analysis_mono_start.show() 6139 self._view.ui.lbl_pred_analysis_mono_images.show() 6140 self._view.ui.cb_pred_analysis_mono_images.show() 6141 # if self._view.ui.list_pred_analysis_mono_overview.count() == 0: 6142 # 6143 # self._view.ui.btn_pred_analysis_mono_back_pred_setup.show() 6144 # self._view.ui.btn_pred_analysis_mono_remove.hide()
Removes a selected protein pair form the list of protein pairs to analyze.
def
check_mono_pred_analysis_if_same_no_of_chains_selected(self) -> None:
6146 def check_mono_pred_analysis_if_same_no_of_chains_selected(self) -> None: 6147 """Checks if the same number of chains were selected.""" 6148 self._view.ui.btn_pred_analysis_mono_next_4.setEnabled(False) 6149 if self.no_of_selected_chains == len(self._view.ui.list_pred_analysis_mono_model_chains.selectedItems()): 6150 self._view.ui.btn_pred_analysis_mono_next_4.setEnabled(True) 6151 6152 prot_1_name = self._view.ui.lbl_pred_analysis_mono_prot_struct_1.text() 6153 prot_1_chains = [] 6154 for chain in self._view.ui.list_pred_analysis_mono_ref_chains.selectedItems(): 6155 prot_1_chains.append(chain.text()) 6156 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 6157 prot_2_name = self._view.ui.lbl_pred_analysis_mono_prot_struct_2.text() 6158 prot_2_chains = [] 6159 for chain in self._view.ui.list_pred_analysis_mono_model_chains.selectedItems(): 6160 prot_2_chains.append(chain.text()) 6161 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 6162 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 6163 for tmp_row in range(self._view.ui.list_pred_analysis_mono_overview.count()): 6164 if analysis_name == self._view.ui.list_pred_analysis_mono_overview.item(tmp_row).text(): 6165 self._view.ui.btn_pred_analysis_mono_next_4.setEnabled(False) 6166 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_mono_next_4) 6167 return
Checks if the same number of chains were selected.
def
check_mono_pred_analysis_if_prot_structs_are_filled(self) -> None:
6169 def check_mono_pred_analysis_if_prot_structs_are_filled(self) -> None: 6170 """Checks if two proteins were selected.""" 6171 prot_1 = self._view.ui.box_pred_analysis_mono_prot_struct_1.itemText( 6172 self._view.ui.box_pred_analysis_mono_prot_struct_1.currentIndex(), 6173 ) 6174 prot_2 = self._view.ui.box_pred_analysis_mono_prot_struct_2.itemText( 6175 self._view.ui.box_pred_analysis_mono_prot_struct_2.currentIndex(), 6176 ) 6177 if prot_1 != "" and prot_2 != "": 6178 self._view.ui.btn_pred_analysis_mono_next_2.setEnabled(True) 6179 else: 6180 self._view.ui.btn_pred_analysis_mono_next_2.setEnabled(False)
Checks if two proteins were selected.
def
count_mono_pred_analysis_selected_chains_for_prot_struct_1(self) -> None:
6182 def count_mono_pred_analysis_selected_chains_for_prot_struct_1(self) -> None: 6183 """Counts the number of chains selected in protein 1.""" 6184 self.no_of_selected_chains = len(self._view.ui.list_pred_analysis_mono_ref_chains.selectedItems()) 6185 if self.no_of_selected_chains > 0: 6186 self._view.ui.btn_pred_analysis_mono_next_3.setEnabled(True) 6187 else: 6188 self._view.ui.btn_pred_analysis_mono_next_3.setEnabled(False)
Counts the number of chains selected in protein 1.
def
switch_monomer_pred_analysis_tab(self) -> None:
6194 def switch_monomer_pred_analysis_tab(self) -> None: 6195 """Switches the tabs from prediction to analysis and vice versa.""" 6196 if self._view.ui.tabWidget.currentIndex() == 0: 6197 # goes from prediction to analysis 6198 self._view.ui.tabWidget.setTabEnabled(1, True) 6199 self._view.ui.tabWidget.setTabEnabled(0, False) 6200 self._view.ui.tabWidget.setCurrentIndex(1) 6201 gui_elements_to_show = [ 6202 self._view.ui.lbl_pred_analysis_mono_overview, 6203 self._view.ui.list_pred_analysis_mono_overview, 6204 self._view.ui.btn_pred_analysis_mono_add, 6205 self._view.ui.btn_pred_analysis_mono_back_pred_setup, 6206 ] 6207 gui_elements_to_hide = [ 6208 self._view.ui.btn_pred_analysis_mono_remove, 6209 self._view.ui.lbl_pred_analysis_mono_prot_struct_1, 6210 self._view.ui.lbl_pred_analysis_mono_prot_struct_2, 6211 self._view.ui.lbl_analysis_batch_vs_2, 6212 self._view.ui.lbl_pred_analysis_mono_ref_chains, 6213 self._view.ui.list_pred_analysis_mono_ref_chains, 6214 self._view.ui.btn_pred_analysis_mono_back_4, 6215 self._view.ui.btn_pred_analysis_mono_next_3, 6216 self._view.ui.box_pred_analysis_mono_prot_struct_1, 6217 self._view.ui.box_pred_analysis_mono_prot_struct_2, 6218 self._view.ui.btn_pred_analysis_mono_back_3, 6219 self._view.ui.btn_pred_analysis_mono_next_2, 6220 self._view.ui.lbl_pred_analysis_mono_model_chains, 6221 self._view.ui.list_pred_analysis_mono_model_chains, 6222 self._view.ui.btn_pred_analysis_mono_back_5, 6223 self._view.ui.btn_pred_analysis_mono_next_4, 6224 self._view.ui.lbl_pred_analysis_mono_images, 6225 self._view.ui.cb_pred_analysis_mono_images, 6226 self._view.ui.btn_pred_analysis_mono_start, 6227 ] 6228 gui_utils.show_gui_elements(gui_elements_to_show) 6229 gui_utils.hide_gui_elements(gui_elements_to_hide) 6230 if self._view.ui.list_pred_analysis_mono_overview.count() > 0: 6231 self._view.ui.btn_pred_analysis_mono_remove.show() 6232 self._view.ui.btn_pred_analysis_mono_remove.setEnabled(False) 6233 self._view.ui.btn_pred_analysis_mono_start.show() 6234 self._view.ui.lbl_pred_analysis_mono_images.show() 6235 self._view.ui.cb_pred_analysis_mono_images.show() 6236 else: 6237 # goes from analysis to prediction 6238 if self._view.ui.list_pred_analysis_mono_overview.count() > 0: 6239 gui_elements_to_show = [ 6240 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 6241 self._view.ui.table_pred_analysis_mono_prot_to_predict, 6242 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 6243 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 6244 ] 6245 gui_elements_to_hide = [ 6246 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 6247 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 6248 self._view.ui.lbl_pred_analysis_mono_prot_name, 6249 self._view.ui.txt_pred_analysis_mono_prot_name, 6250 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 6251 self._view.ui.btn_pred_analysis_mono_back, 6252 self._view.ui.btn_pred_analysis_mono_next, 6253 self._view.ui.lbl_pred_analysis_mono_seq_name, 6254 self._view.ui.txt_pred_analysis_mono_seq_name, 6255 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 6256 self._view.ui.btn_pred_analysis_mono_back_2, 6257 self._view.ui.btn_pred_analysis_mono_add_protein, 6258 self._view.ui.lbl_pred_mono_advanced_config_2, 6259 self._view.ui.btn_pred_mono_advanced_config_2, 6260 ] 6261 gui_utils.show_gui_elements(gui_elements_to_show) 6262 gui_utils.hide_gui_elements(gui_elements_to_hide) 6263 else: 6264 gui_elements_to_show = [ 6265 self._view.ui.lbl_pred_analysis_mono_prot_to_predict, 6266 self._view.ui.table_pred_analysis_mono_prot_to_predict, 6267 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove, 6268 self._view.ui.btn_pred_analysis_mono_seq_to_predict, 6269 self._view.ui.lbl_pred_mono_advanced_config_2, 6270 self._view.ui.btn_pred_mono_advanced_config_2, 6271 self._view.ui.btn_pred_analysis_mono_go_analysis_setup, 6272 self._view.ui.lbl_pred_analysis_mono_to_analysis_setup, 6273 ] 6274 gui_elements_to_hide = [ 6275 self._view.ui.lbl_pred_analysis_mono_prot_name, 6276 self._view.ui.txt_pred_analysis_mono_prot_name, 6277 self._view.ui.lbl_pred_analysis_mono_prot_name_status, 6278 self._view.ui.btn_pred_analysis_mono_back, 6279 self._view.ui.btn_pred_analysis_mono_next, 6280 self._view.ui.lbl_pred_analysis_mono_seq_name, 6281 self._view.ui.txt_pred_analysis_mono_seq_name, 6282 self._view.ui.lbl_pred_analysis_mono_seq_name_status, 6283 self._view.ui.btn_pred_analysis_mono_back_2, 6284 self._view.ui.btn_pred_analysis_mono_add_protein, 6285 ] 6286 gui_utils.show_gui_elements(gui_elements_to_show) 6287 gui_utils.hide_gui_elements(gui_elements_to_hide) 6288 self._view.ui.btn_pred_analysis_mono_seq_to_predict_remove.setEnabled(False) 6289 self._view.ui.tabWidget.setTabEnabled(0, True) 6290 self._view.ui.tabWidget.setTabEnabled(1, False) 6291 self._view.ui.tabWidget.setCurrentIndex(0)
Switches the tabs from prediction to analysis and vice versa.
def
display_multimer_pred_analysis(self) -> None:
6322 def display_multimer_pred_analysis(self) -> None: 6323 """Displays the multimer prediction + analysis page.""" 6324 # checks internet connection 6325 if not tools.check_internet_connectivity(): 6326 gui_utils.no_internet_dialog() 6327 return 6328 6329 self._init_multi_pred_analysis_page() 6330 self._view.ui.table_pred_analysis_multi_prot_to_predict.clear() 6331 self._view.ui.table_pred_analysis_multi_prot_to_predict.setHorizontalHeaderItem( 6332 0, 6333 QtWidgets.QTableWidgetItem("Chain"), 6334 ) 6335 self._view.ui.table_pred_analysis_multi_prot_to_predict.setHorizontalHeaderItem( 6336 1, 6337 QtWidgets.QTableWidgetItem("Sequence"), 6338 ) 6339 self._view.ui.table_pred_analysis_multi_prot_to_predict.resizeColumnsToContents() 6340 gui_elements_to_show = [ 6341 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6342 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6343 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6344 ] 6345 gui_elements_to_hide = [ 6346 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6347 self._view.ui.lbl_pred_analysis_multi_prot_name, 6348 self._view.ui.txt_pred_analysis_multi_prot_name, 6349 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6350 self._view.ui.btn_pred_analysis_multi_back, 6351 self._view.ui.btn_pred_analysis_multi_next, 6352 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6353 self._view.ui.txt_pred_analysis_multi_prot_seq, 6354 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6355 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6356 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6357 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6358 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6359 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6360 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6361 self._view.ui.btn_pred_analysis_multi_back_2, 6362 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6363 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6364 self._view.ui.btn_pred_analysis_multi_advanced_config, 6365 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6366 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6367 ] 6368 gui_utils.show_gui_elements(gui_elements_to_show) 6369 gui_utils.hide_gui_elements(gui_elements_to_hide) 6370 if self._view.ui.tabWidget_2.currentIndex() == 1: 6371 self._view.ui.tabWidget_2.setCurrentIndex(0) 6372 self._view.ui.tabWidget_2.setTabEnabled(1, False) 6373 self._view.ui.tabWidget_2.setTabEnabled(0, True) 6374 tools.switch_page( 6375 self._view.ui.stackedWidget, 6376 self._view.ui.lbl_page_title, 6377 22, 6378 "Multimer Prediction + Analysis", 6379 ) 6380 self.last_sidebar_button = styles.color_sidebar_buttons( 6381 self.last_sidebar_button, 6382 self._view.ui.btn_pred_analysis_multimer_page, 6383 ) 6384 self._view.ui.table_pred_analysis_multi_prot_to_predict.setEnabled(True)
Displays the multimer prediction + analysis page.
def
multi_pred_analysis_validate_protein_name(self) -> None:
6387 def multi_pred_analysis_validate_protein_name(self) -> None: 6388 """Validates the input of the protein name in real-time.""" 6389 if safeguard.Safeguard.check_if_value_is_in_table_v_header( 6390 self._view.ui.txt_pred_analysis_multi_prot_name.text(), 6391 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6392 ): 6393 self._view.ui.lbl_pred_analysis_multi_prot_name_status.setText("Protein name already used.") 6394 self._view.ui.btn_pred_analysis_multi_next.setEnabled(False) 6395 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_multi_next) 6396 else: 6397 self._view.ui.btn_pred_analysis_multi_next.setEnabled(True) 6398 tools.validate_protein_name( 6399 self._view.ui.txt_pred_analysis_multi_prot_name, 6400 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6401 self._view.ui.btn_pred_analysis_multi_next, 6402 )
Validates the input of the protein name in real-time.
def
multi_pred_analysis_validate_protein_sequence(self) -> None:
6404 def multi_pred_analysis_validate_protein_sequence(self) -> None: 6405 """Validates the input of the protein sequence in real-time.""" 6406 tools.validate_protein_sequence( 6407 self._view.ui.txt_pred_analysis_multi_prot_seq, 6408 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6409 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6410 )
Validates the input of the protein sequence in real-time.
def
multi_pred_analysis_check_if_list_is_empty(self) -> None:
6412 def multi_pred_analysis_check_if_list_is_empty(self) -> None: 6413 """Checks if the list of sequences of the protein is empty.""" 6414 if self._view.ui.list_pred_analysis_multi_prot_seq_overview.count() == 0: 6415 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2.setEnabled(False) 6416 else: 6417 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2.setEnabled(True)
Checks if the list of sequences of the protein is empty.
def
multi_pred_analysis_add_sequence_to_list(self) -> None:
6419 def multi_pred_analysis_add_sequence_to_list(self) -> None: 6420 """Adds the entered sequence to the sequences of the protein.""" 6421 self._view.ui.list_pred_analysis_multi_prot_seq_overview.addItem( 6422 QtWidgets.QListWidgetItem(self._view.ui.txt_pred_analysis_multi_prot_seq.toPlainText()), 6423 ) 6424 self.multi_pred_analysis_check_if_list_is_empty()
Adds the entered sequence to the sequences of the protein.
def
multi_pred_analysis_remove_sequence_to_list(self) -> None:
6426 def multi_pred_analysis_remove_sequence_to_list(self) -> None: 6427 """Removes the entered sequence from the sequences of the protein.""" 6428 self._view.ui.list_pred_analysis_multi_prot_seq_overview.takeItem( 6429 self._view.ui.list_pred_analysis_multi_prot_seq_overview.currentRow(), 6430 ) 6431 self.multi_pred_analysis_check_if_list_is_empty() 6432 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove.setEnabled(False)
Removes the entered sequence from the sequences of the protein.
def
multi_pred_analysis_check_if_table_is_empty(self) -> None:
6434 def multi_pred_analysis_check_if_table_is_empty(self) -> None: 6435 """Checks if the list of proteins to predict is empty.""" 6436 if self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() == 0: 6437 styles.color_button_not_ready(self._view.ui.btn_pred_multi_predict) 6438 gui_elements_to_show = [ 6439 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6440 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6441 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6442 ] 6443 gui_elements_to_hide = [ 6444 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6445 self._view.ui.lbl_pred_analysis_multi_prot_name, 6446 self._view.ui.txt_pred_analysis_multi_prot_name, 6447 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6448 self._view.ui.btn_pred_analysis_multi_back, 6449 self._view.ui.btn_pred_analysis_multi_next, 6450 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6451 self._view.ui.txt_pred_analysis_multi_prot_seq, 6452 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6453 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6454 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6455 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6456 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6457 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6458 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6459 self._view.ui.btn_pred_analysis_multi_back_2, 6460 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6461 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6462 self._view.ui.btn_pred_analysis_multi_advanced_config, 6463 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6464 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6465 ] 6466 gui_utils.show_gui_elements(gui_elements_to_show) 6467 gui_utils.hide_gui_elements(gui_elements_to_hide) 6468 self._view.ui.btn_pred_multi_predict.setEnabled(False) 6469 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False) 6470 else: 6471 self._view.ui.btn_pred_multi_predict.setEnabled(True) 6472 gui_elements_to_show = [ 6473 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6474 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6475 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6476 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6477 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6478 self._view.ui.btn_pred_analysis_multi_advanced_config, 6479 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6480 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6481 ] 6482 gui_elements_to_hide = [ 6483 self._view.ui.lbl_pred_analysis_multi_prot_name, 6484 self._view.ui.txt_pred_analysis_multi_prot_name, 6485 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6486 self._view.ui.btn_pred_analysis_multi_back, 6487 self._view.ui.btn_pred_analysis_multi_next, 6488 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6489 self._view.ui.txt_pred_analysis_multi_prot_seq, 6490 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6491 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6492 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6493 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6494 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6495 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6496 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6497 self._view.ui.btn_pred_analysis_multi_back_2, 6498 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6499 ] 6500 gui_utils.show_gui_elements(gui_elements_to_show) 6501 gui_utils.hide_gui_elements(gui_elements_to_hide) 6502 self._view.ui.btn_pred_multi_prot_to_predict_remove.setEnabled(False)
Checks if the list of proteins to predict is empty.
def
multi_pred_analysis_add_protein_to_predict(self) -> None:
6504 def multi_pred_analysis_add_protein_to_predict(self) -> None: 6505 """Adds the proteins to the list of proteins to predict.""" 6506 for i in range(self._view.ui.list_pred_analysis_multi_prot_seq_overview.count()): 6507 self._view.ui.table_pred_analysis_multi_prot_to_predict.setRowCount( 6508 self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() + 1, 6509 ) 6510 self._view.ui.table_pred_analysis_multi_prot_to_predict.insertRow( 6511 self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() + 1, 6512 ) 6513 tmp_chain_seq = ( 6514 constants.chain_dict.get(i), 6515 self._view.ui.list_pred_analysis_multi_prot_seq_overview.item(i).text(), 6516 ) 6517 self._view.ui.table_pred_analysis_multi_prot_to_predict.setItem( 6518 self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() - 1, 6519 0, 6520 QtWidgets.QTableWidgetItem(tmp_chain_seq[0]), 6521 ) 6522 self._view.ui.table_pred_analysis_multi_prot_to_predict.setItem( 6523 self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() - 1, 6524 1, 6525 QtWidgets.QTableWidgetItem(tmp_chain_seq[1]), 6526 ) 6527 name_item = QtWidgets.QTableWidgetItem(self._view.ui.txt_pred_analysis_multi_prot_name.text()) 6528 self._view.ui.table_pred_analysis_multi_prot_to_predict.setVerticalHeaderItem( 6529 self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() - 1, 6530 name_item, 6531 ) 6532 self._view.ui.table_pred_analysis_multi_prot_to_predict.resizeColumnsToContents() 6533 self.multi_pred_analysis_check_if_table_is_empty() 6534 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove.setEnabled(False)
Adds the proteins to the list of proteins to predict.
def
multi_pred_analysis_remove_protein_to_predict(self) -> None:
6536 def multi_pred_analysis_remove_protein_to_predict(self) -> None: 6537 """Removes the selected protein from the list of proteins to predict.""" 6538 if self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() == 1: 6539 self._view.ui.table_pred_analysis_multi_prot_to_predict.removeRow(0) 6540 else: 6541 self._view.ui.table_pred_analysis_multi_prot_to_predict.removeRow( 6542 self._view.ui.table_pred_analysis_multi_prot_to_predict.currentRow(), 6543 ) 6544 prot_name = self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem( 6545 self._view.ui.table_pred_analysis_multi_prot_to_predict.currentRow(), 6546 ).text() 6547 for i in range(self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount()): 6548 if self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem(i).text() == prot_name: 6549 self._view.ui.table_pred_analysis_multi_prot_to_predict.setItem( 6550 i, 6551 0, 6552 QtWidgets.QTableWidgetItem(constants.chain_dict.get(i)), 6553 ) 6554 self.multi_pred_analysis_check_if_table_is_empty() 6555 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove.setEnabled(False)
Removes the selected protein from the list of proteins to predict.
def
multi_pred_analysis_add(self) -> None:
6557 def multi_pred_analysis_add(self) -> None: 6558 """Shows the gui elements for the protein name.""" 6559 gui_elements_to_show = [ 6560 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6561 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6562 self._view.ui.lbl_pred_analysis_multi_prot_name, 6563 self._view.ui.txt_pred_analysis_multi_prot_name, 6564 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6565 self._view.ui.btn_pred_analysis_multi_back, 6566 self._view.ui.btn_pred_analysis_multi_next, 6567 ] 6568 gui_elements_to_hide = [ 6569 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6570 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6571 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6572 self._view.ui.txt_pred_analysis_multi_prot_seq, 6573 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6574 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6575 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6576 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6577 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6578 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6579 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6580 self._view.ui.btn_pred_analysis_multi_back_2, 6581 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6582 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6583 self._view.ui.btn_pred_analysis_multi_advanced_config, 6584 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6585 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6586 ] 6587 gui_utils.show_gui_elements(gui_elements_to_show) 6588 gui_utils.hide_gui_elements(gui_elements_to_hide) 6589 gui_utils.enable_text_box( 6590 self._view.ui.txt_pred_analysis_multi_prot_name, 6591 self._view.ui.lbl_pred_analysis_multi_prot_name, 6592 ) 6593 gui_utils.disable_text_box( 6594 self._view.ui.txt_pred_analysis_multi_prot_seq, 6595 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6596 ) 6597 self._view.ui.btn_pred_analysis_multi_next.setEnabled(False) 6598 self._view.ui.txt_pred_analysis_multi_prot_name.clear() 6599 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_multi_next) 6600 if self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount() > 0: 6601 try: 6602 self._view.ui.table_pred_analysis_multi_prot_to_predict.currentItem().setSelected(False) 6603 except AttributeError: 6604 constants.PYSSA_LOGGER.debug("No selection on Local Multimer Prediction in overview table.")
Shows the gui elements for the protein name.
def
multi_pred_analysis_back(self) -> None:
6606 def multi_pred_analysis_back(self) -> None: 6607 """Hides the gui elements for the protein name.""" 6608 gui_elements_to_show = [ 6609 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6610 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6611 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6612 ] 6613 gui_elements_to_hide = [ 6614 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6615 self._view.ui.lbl_pred_analysis_multi_prot_name, 6616 self._view.ui.txt_pred_analysis_multi_prot_name, 6617 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6618 self._view.ui.btn_pred_analysis_multi_back, 6619 self._view.ui.btn_pred_analysis_multi_next, 6620 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6621 self._view.ui.txt_pred_analysis_multi_prot_seq, 6622 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6623 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6624 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6625 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6626 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6627 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6628 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6629 self._view.ui.btn_pred_analysis_multi_back_2, 6630 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6631 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6632 self._view.ui.btn_pred_analysis_multi_advanced_config, 6633 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6634 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6635 ] 6636 gui_utils.show_gui_elements(gui_elements_to_show) 6637 gui_utils.hide_gui_elements(gui_elements_to_hide) 6638 self.multi_pred_analysis_check_if_table_is_empty()
Hides the gui elements for the protein name.
def
multi_pred_analysis_next(self) -> None:
6640 def multi_pred_analysis_next(self) -> None: 6641 """Shows the gui elements for the protein sequence.""" 6642 gui_elements_to_show = [ 6643 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6644 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6645 self._view.ui.lbl_pred_analysis_multi_prot_name, 6646 self._view.ui.txt_pred_analysis_multi_prot_name, 6647 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6648 self._view.ui.txt_pred_analysis_multi_prot_seq, 6649 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6650 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6651 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6652 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6653 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6654 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6655 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6656 self._view.ui.btn_pred_analysis_multi_back_2, 6657 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6658 ] 6659 gui_elements_to_hide = [ 6660 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6661 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6662 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6663 self._view.ui.btn_pred_analysis_multi_back, 6664 self._view.ui.btn_pred_analysis_multi_next, 6665 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6666 self._view.ui.btn_pred_analysis_multi_advanced_config, 6667 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6668 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6669 ] 6670 gui_utils.show_gui_elements(gui_elements_to_show) 6671 gui_utils.hide_gui_elements(gui_elements_to_hide) 6672 gui_utils.enable_text_box( 6673 self._view.ui.txt_pred_analysis_multi_prot_seq, 6674 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6675 ) 6676 gui_utils.disable_text_box( 6677 self._view.ui.txt_pred_analysis_multi_prot_name, 6678 self._view.ui.lbl_pred_analysis_multi_prot_name, 6679 ) 6680 self._view.ui.txt_pred_analysis_multi_prot_seq.clear() 6681 self._view.ui.list_pred_analysis_multi_prot_seq_overview.clear() 6682 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2.setEnabled(False) 6683 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove.setEnabled(False) 6684 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2)
Shows the gui elements for the protein sequence.
def
multi_pred_analysis_back_2(self) -> None:
6686 def multi_pred_analysis_back_2(self) -> None: 6687 """Hides the gui elements for the protein sequence.""" 6688 gui_elements_to_show = [ 6689 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6690 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6691 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6692 self._view.ui.btn_pred_analysis_multi_back, 6693 self._view.ui.btn_pred_analysis_multi_next, 6694 self._view.ui.lbl_pred_analysis_multi_prot_name, 6695 self._view.ui.txt_pred_analysis_multi_prot_name, 6696 ] 6697 gui_elements_to_hide = [ 6698 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6699 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6700 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6701 self._view.ui.txt_pred_analysis_multi_prot_seq, 6702 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6703 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6704 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6705 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6706 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6707 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6708 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6709 self._view.ui.btn_pred_analysis_multi_back_2, 6710 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6711 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6712 self._view.ui.btn_pred_analysis_multi_advanced_config, 6713 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6714 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6715 ] 6716 gui_utils.show_gui_elements(gui_elements_to_show) 6717 gui_utils.hide_gui_elements(gui_elements_to_hide) 6718 gui_utils.enable_text_box( 6719 self._view.ui.txt_pred_analysis_multi_prot_name, 6720 self._view.ui.lbl_pred_analysis_multi_prot_name, 6721 ) 6722 gui_utils.disable_text_box( 6723 self._view.ui.txt_pred_analysis_multi_prot_seq, 6724 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6725 )
Hides the gui elements for the protein sequence.
def
multi_pred_analysis_prot_seq_overview_item_changed(self) -> None:
6727 def multi_pred_analysis_prot_seq_overview_item_changed(self) -> None: 6728 """Enables the remove button of the list of sequences of the protein.""" 6729 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove.setEnabled(True)
Enables the remove button of the list of sequences of the protein.
def
multi_pred_analysis_prot_to_predict_item_changed(self) -> None:
6731 def multi_pred_analysis_prot_to_predict_item_changed(self) -> None: 6732 """Enables the remove button of the list of proteins to predict.""" 6733 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove.setEnabled(True)
Enables the remove button of the list of proteins to predict.
def
switch_multimer_pred_analysis_tab(self) -> None:
6737 def switch_multimer_pred_analysis_tab(self) -> None: 6738 """Switches the tabs from prediction to analysis and vice versa.""" 6739 if self._view.ui.tabWidget_2.currentIndex() == 0: 6740 # goes from prediction to analysis 6741 self._view.ui.tabWidget_2.setCurrentIndex(1) 6742 gui_elements_to_show = [ 6743 self._view.ui.lbl_pred_analysis_multi_overview, 6744 self._view.ui.list_pred_analysis_multi_overview, 6745 self._view.ui.btn_pred_analysis_multi_add, 6746 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 6747 ] 6748 gui_elements_to_hide = [ 6749 self._view.ui.btn_pred_analysis_multi_remove, 6750 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 6751 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 6752 self._view.ui.lbl_analysis_batch_vs_3, 6753 self._view.ui.lbl_pred_analysis_multi_ref_chains, 6754 self._view.ui.list_pred_analysis_multi_ref_chains, 6755 self._view.ui.btn_pred_analysis_multi_back_4, 6756 self._view.ui.btn_pred_analysis_multi_next_3, 6757 self._view.ui.box_pred_analysis_multi_prot_struct_1, 6758 self._view.ui.box_pred_analysis_multi_prot_struct_2, 6759 self._view.ui.btn_pred_analysis_multi_back_3, 6760 self._view.ui.btn_pred_analysis_multi_next_2, 6761 self._view.ui.lbl_pred_analysis_multi_model_chains, 6762 self._view.ui.list_pred_analysis_multi_model_chains, 6763 self._view.ui.btn_pred_analysis_multi_back_5, 6764 self._view.ui.btn_pred_analysis_multi_next_4, 6765 self._view.ui.lbl_pred_analysis_multi_images, 6766 self._view.ui.cb_pred_analysis_multi_images, 6767 self._view.ui.btn_pred_analysis_multi_start, 6768 ] 6769 gui_utils.show_gui_elements(gui_elements_to_show) 6770 gui_utils.hide_gui_elements(gui_elements_to_hide) 6771 self._view.ui.tabWidget_2.setTabEnabled(1, True) 6772 self._view.ui.tabWidget_2.setTabEnabled(0, False) 6773 if self._view.ui.list_pred_analysis_multi_overview.count() > 0: 6774 self._view.ui.btn_pred_analysis_multi_remove.show() 6775 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(False) 6776 self._view.ui.btn_pred_analysis_multi_start.show() 6777 self._view.ui.lbl_pred_analysis_multi_images.show() 6778 self._view.ui.cb_pred_analysis_multi_images.show() 6779 else: 6780 # goes from analysis to prediction 6781 self._view.ui.tabWidget_2.setCurrentIndex(0) 6782 if self._view.ui.list_pred_analysis_multi_overview.count() > 0: 6783 gui_elements_to_show = [ 6784 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6785 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6786 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6787 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6788 ] 6789 gui_elements_to_hide = [ 6790 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6791 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6792 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6793 self._view.ui.btn_pred_analysis_multi_advanced_config, 6794 self._view.ui.lbl_pred_analysis_multi_prot_name, 6795 self._view.ui.txt_pred_analysis_multi_prot_name, 6796 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6797 self._view.ui.btn_pred_analysis_multi_back, 6798 self._view.ui.btn_pred_analysis_multi_next, 6799 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6800 self._view.ui.txt_pred_analysis_multi_prot_seq, 6801 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6802 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6803 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6804 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6805 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6806 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6807 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6808 self._view.ui.btn_pred_analysis_multi_back_2, 6809 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6810 ] 6811 gui_utils.show_gui_elements(gui_elements_to_show) 6812 gui_utils.hide_gui_elements(gui_elements_to_hide) 6813 else: 6814 gui_elements_to_show = [ 6815 self._view.ui.lbl_pred_analysis_multi_prot_to_predict, 6816 self._view.ui.table_pred_analysis_multi_prot_to_predict, 6817 self._view.ui.btn_pred_analysis_multi_prot_to_predict_remove, 6818 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add, 6819 self._view.ui.lbl_pred_analysis_multi_advanced_config, 6820 self._view.ui.btn_pred_analysis_multi_advanced_config, 6821 self._view.ui.btn_pred_analysis_multi_go_analysis_setup, 6822 self._view.ui.lbl_pred_analysis_multi_to_analysis_setup, 6823 ] 6824 gui_elements_to_hide = [ 6825 self._view.ui.lbl_pred_analysis_multi_prot_name, 6826 self._view.ui.txt_pred_analysis_multi_prot_name, 6827 self._view.ui.lbl_pred_analysis_multi_prot_name_status, 6828 self._view.ui.btn_pred_analysis_multi_back, 6829 self._view.ui.btn_pred_analysis_multi_next, 6830 self._view.ui.lbl_pred_analysis_multi_prot_seq, 6831 self._view.ui.txt_pred_analysis_multi_prot_seq, 6832 self._view.ui.lbl_pred_analysis_multi_prot_seq_status, 6833 self._view.ui.lbl_pred_multi_prot_seq_add_2, 6834 self._view.ui.btn_pred_analysis_multi_prot_seq_add, 6835 self._view.ui.lbl_pred_analysis_multi_prot_seq_overview, 6836 self._view.ui.list_pred_analysis_multi_prot_seq_overview, 6837 self._view.ui.btn_pred_analysis_multi_prot_seq_overview_remove, 6838 self._view.ui.lbl_pred_analysis_multi_prot_to_predict_2, 6839 self._view.ui.btn_pred_analysis_multi_back_2, 6840 self._view.ui.btn_pred_analysis_multi_prot_to_predict_add_2, 6841 ] 6842 gui_utils.show_gui_elements(gui_elements_to_show) 6843 gui_utils.hide_gui_elements(gui_elements_to_hide) 6844 self._view.ui.tabWidget_2.setTabEnabled(0, True) 6845 self._view.ui.tabWidget_2.setTabEnabled(1, False)
Switches the tabs from prediction to analysis and vice versa.
def
multi_pred_analysis_structure_analysis_add(self) -> None:
6848 def multi_pred_analysis_structure_analysis_add(self) -> None: 6849 """Shows the gui elements to choose the two proteins.""" 6850 gui_elements_to_show = [ 6851 self._view.ui.lbl_pred_analysis_multi_overview, 6852 self._view.ui.list_pred_analysis_multi_overview, 6853 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 6854 self._view.ui.box_pred_analysis_multi_prot_struct_1, 6855 self._view.ui.lbl_analysis_batch_vs_3, 6856 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 6857 self._view.ui.box_pred_analysis_multi_prot_struct_2, 6858 self._view.ui.btn_pred_analysis_multi_back_3, 6859 self._view.ui.btn_pred_analysis_multi_next_2, 6860 ] 6861 gui_elements_to_hide = [ 6862 self._view.ui.btn_pred_analysis_multi_remove, 6863 self._view.ui.btn_pred_analysis_multi_add, 6864 self._view.ui.lbl_pred_analysis_multi_ref_chains, 6865 self._view.ui.list_pred_analysis_multi_ref_chains, 6866 self._view.ui.btn_pred_analysis_multi_back_4, 6867 self._view.ui.btn_pred_analysis_multi_next_3, 6868 self._view.ui.lbl_pred_analysis_multi_model_chains, 6869 self._view.ui.list_pred_analysis_multi_model_chains, 6870 self._view.ui.btn_pred_analysis_multi_back_5, 6871 self._view.ui.btn_pred_analysis_multi_next_4, 6872 self._view.ui.lbl_pred_analysis_multi_images, 6873 self._view.ui.cb_pred_analysis_multi_images, 6874 self._view.ui.btn_pred_analysis_multi_start, 6875 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 6876 ] 6877 gui_utils.show_gui_elements(gui_elements_to_show) 6878 gui_utils.hide_gui_elements(gui_elements_to_hide) 6879 self._view.ui.lbl_pred_analysis_multi_prot_struct_1.clear() 6880 self._view.ui.lbl_pred_analysis_multi_prot_struct_2.clear() 6881 self._view.ui.lbl_pred_analysis_multi_prot_struct_1.setText("Protein structure 1") 6882 self._view.ui.lbl_pred_analysis_multi_prot_struct_2.setText("Protein structure 2") 6883 self.fill_multi_pred_analysis_protein_boxes() 6884 if self._view.ui.list_pred_analysis_multi_overview.count() > 0: 6885 try: 6886 self._view.ui.list_pred_analysis_multi_overview.currentItem().setSelected(False) 6887 except AttributeError: 6888 constants.PYSSA_LOGGER.debug("No selection in struction analysis overview.")
Shows the gui elements to choose the two proteins.
def
multi_pred_analysis_structure_analysis_back_3(self) -> None:
6890 def multi_pred_analysis_structure_analysis_back_3(self) -> None: 6891 """Hides the gui elements to choose the two proteins.""" 6892 gui_elements_to_show = [ 6893 self._view.ui.lbl_pred_analysis_multi_overview, 6894 self._view.ui.list_pred_analysis_multi_overview, 6895 self._view.ui.btn_pred_analysis_multi_add, 6896 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 6897 ] 6898 gui_elements_to_hide = [ 6899 self._view.ui.btn_pred_analysis_multi_remove, 6900 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 6901 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 6902 self._view.ui.lbl_analysis_batch_vs_3, 6903 self._view.ui.lbl_pred_analysis_multi_ref_chains, 6904 self._view.ui.list_pred_analysis_multi_ref_chains, 6905 self._view.ui.btn_pred_analysis_multi_back_4, 6906 self._view.ui.btn_pred_analysis_multi_next_3, 6907 self._view.ui.box_pred_analysis_multi_prot_struct_1, 6908 self._view.ui.box_pred_analysis_multi_prot_struct_2, 6909 self._view.ui.btn_pred_analysis_multi_back_3, 6910 self._view.ui.btn_pred_analysis_multi_next_2, 6911 self._view.ui.lbl_pred_analysis_multi_model_chains, 6912 self._view.ui.list_pred_analysis_multi_model_chains, 6913 self._view.ui.btn_pred_analysis_multi_back_5, 6914 self._view.ui.btn_pred_analysis_multi_next_4, 6915 self._view.ui.lbl_pred_analysis_multi_images, 6916 self._view.ui.cb_pred_analysis_multi_images, 6917 self._view.ui.btn_pred_analysis_multi_start, 6918 ] 6919 gui_utils.show_gui_elements(gui_elements_to_show) 6920 gui_utils.hide_gui_elements(gui_elements_to_hide) 6921 if self._view.ui.list_pred_analysis_multi_overview.count() > 0: 6922 self._view.ui.btn_pred_analysis_multi_remove.show() 6923 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(False) 6924 self._view.ui.btn_pred_analysis_multi_start.show() 6925 self._view.ui.lbl_pred_analysis_multi_images.show() 6926 self._view.ui.cb_pred_analysis_multi_images.show()
Hides the gui elements to choose the two proteins.
def
multi_pred_analysis_structure_analysis_next_3(self) -> None:
6928 def multi_pred_analysis_structure_analysis_next_3(self) -> None: 6929 """Shows the gui elements to select the chains in protein 2.""" 6930 gui_elements_to_show = [ 6931 self._view.ui.lbl_pred_analysis_multi_overview, 6932 self._view.ui.list_pred_analysis_multi_overview, 6933 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 6934 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 6935 self._view.ui.lbl_analysis_batch_vs_3, 6936 self._view.ui.lbl_pred_analysis_multi_ref_chains, 6937 self._view.ui.list_pred_analysis_multi_ref_chains, 6938 self._view.ui.lbl_pred_analysis_multi_model_chains, 6939 self._view.ui.list_pred_analysis_multi_model_chains, 6940 self._view.ui.btn_pred_analysis_multi_back_5, 6941 self._view.ui.btn_pred_analysis_multi_next_4, 6942 ] 6943 gui_elements_to_hide = [ 6944 self._view.ui.btn_pred_analysis_multi_remove, 6945 self._view.ui.btn_pred_analysis_multi_add, 6946 self._view.ui.box_pred_analysis_multi_prot_struct_1, 6947 self._view.ui.box_pred_analysis_multi_prot_struct_2, 6948 self._view.ui.btn_pred_analysis_multi_back_3, 6949 self._view.ui.btn_pred_analysis_multi_next_2, 6950 self._view.ui.btn_pred_analysis_multi_back_4, 6951 self._view.ui.btn_pred_analysis_multi_next_3, 6952 self._view.ui.lbl_pred_analysis_multi_images, 6953 self._view.ui.cb_pred_analysis_multi_images, 6954 self._view.ui.btn_pred_analysis_multi_start, 6955 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 6956 ] 6957 gui_utils.show_gui_elements(gui_elements_to_show) 6958 gui_utils.hide_gui_elements(gui_elements_to_hide) 6959 self._view.ui.list_pred_analysis_multi_model_chains.clear() 6960 self._view.ui.list_pred_analysis_multi_ref_chains.setEnabled(False) 6961 self._view.ui.btn_pred_analysis_multi_next_4.setEnabled(False) 6962 6963 for i in range(self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount()): 6964 if ( 6965 self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem(i).text() 6966 == self._view.ui.box_pred_analysis_multi_prot_struct_2.currentText() 6967 ): 6968 self._view.ui.list_pred_analysis_multi_model_chains.addItem( 6969 self._view.ui.table_pred_analysis_multi_prot_to_predict.item(i, 0).text(), 6970 ) 6971 if self._view.ui.list_pred_analysis_multi_model_chains.count() == 0: 6972 tmp_protein = self._current_project.search_protein( 6973 self._view.ui.box_pred_analysis_multi_prot_struct_2.currentText(), 6974 ) 6975 for tmp_chain in tmp_protein.chains: 6976 if tmp_chain.chain_type == "protein_chain": 6977 self._view.ui.list_pred_analysis_multi_model_chains.addItem(tmp_chain.chain_letter) 6978 if len(self._view.ui.list_pred_analysis_multi_ref_chains.selectedItems()) == 1: 6979 self._view.ui.lbl_pred_analysis_multi_model_chains.setText( 6980 f"Select 1 chain in protein structure {self._view.ui.lbl_pred_analysis_multi_prot_struct_2.text()}.", 6981 ) 6982 else: 6983 self._view.ui.lbl_pred_analysis_multi_model_chains.setText( 6984 f"Select {len(self._view.ui.list_pred_analysis_multi_ref_chains.selectedItems())} chains in " 6985 f"protein structure {self._view.ui.lbl_pred_analysis_multi_prot_struct_2.text()}.", 6986 )
Shows the gui elements to select the chains in protein 2.
def
multi_pred_analysis_structure_analysis_back_4(self) -> None:
6988 def multi_pred_analysis_structure_analysis_back_4(self) -> None: 6989 """Hides the gui elements to select the chains in protein 1.""" 6990 gui_elements_to_show = [ 6991 self._view.ui.lbl_pred_analysis_multi_overview, 6992 self._view.ui.list_pred_analysis_multi_overview, 6993 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 6994 self._view.ui.box_pred_analysis_multi_prot_struct_1, 6995 self._view.ui.lbl_analysis_batch_vs_3, 6996 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 6997 self._view.ui.box_pred_analysis_multi_prot_struct_2, 6998 self._view.ui.btn_pred_analysis_multi_back_3, 6999 self._view.ui.btn_pred_analysis_multi_next_2, 7000 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 7001 ] 7002 gui_elements_to_hide = [ 7003 self._view.ui.btn_pred_analysis_multi_remove, 7004 self._view.ui.btn_pred_analysis_multi_add, 7005 self._view.ui.lbl_pred_analysis_multi_ref_chains, 7006 self._view.ui.list_pred_analysis_multi_ref_chains, 7007 self._view.ui.btn_pred_analysis_multi_back_4, 7008 self._view.ui.btn_pred_analysis_multi_next_3, 7009 self._view.ui.lbl_pred_analysis_multi_model_chains, 7010 self._view.ui.list_pred_analysis_multi_model_chains, 7011 self._view.ui.btn_pred_analysis_multi_back_5, 7012 self._view.ui.btn_pred_analysis_multi_next_4, 7013 self._view.ui.lbl_pred_analysis_multi_images, 7014 self._view.ui.cb_pred_analysis_multi_images, 7015 self._view.ui.btn_pred_analysis_multi_start, 7016 ] 7017 gui_utils.show_gui_elements(gui_elements_to_show) 7018 gui_utils.hide_gui_elements(gui_elements_to_hide) 7019 self._view.ui.lbl_pred_analysis_multi_prot_struct_1.setText("Protein structure 1") 7020 self._view.ui.lbl_pred_analysis_multi_prot_struct_2.setText("Protein structure 2")
Hides the gui elements to select the chains in protein 1.
def
multi_pred_analysis_structure_analysis_next_4(self) -> None:
7022 def multi_pred_analysis_structure_analysis_next_4(self) -> None: 7023 """Adds the protein pair to the list of protein pairs to analyze.""" 7024 gui_elements_to_show = [ 7025 self._view.ui.btn_pred_analysis_multi_remove, 7026 self._view.ui.btn_pred_analysis_multi_add, 7027 self._view.ui.lbl_pred_analysis_multi_overview, 7028 self._view.ui.list_pred_analysis_multi_overview, 7029 self._view.ui.lbl_pred_analysis_multi_images, 7030 self._view.ui.cb_pred_analysis_multi_images, 7031 self._view.ui.btn_pred_analysis_multi_start, 7032 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 7033 ] 7034 gui_elements_to_hide = [ 7035 self._view.ui.box_pred_analysis_multi_prot_struct_1, 7036 self._view.ui.box_pred_analysis_multi_prot_struct_2, 7037 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 7038 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 7039 self._view.ui.lbl_analysis_batch_vs_3, 7040 self._view.ui.lbl_pred_analysis_multi_ref_chains, 7041 self._view.ui.list_pred_analysis_multi_ref_chains, 7042 self._view.ui.lbl_pred_analysis_multi_model_chains, 7043 self._view.ui.list_pred_analysis_multi_model_chains, 7044 self._view.ui.btn_pred_analysis_multi_back_3, 7045 self._view.ui.btn_pred_analysis_multi_next_2, 7046 self._view.ui.btn_pred_analysis_multi_back_4, 7047 self._view.ui.btn_pred_analysis_multi_next_3, 7048 self._view.ui.btn_pred_analysis_multi_back_5, 7049 self._view.ui.btn_pred_analysis_multi_next_4, 7050 ] 7051 gui_utils.show_gui_elements(gui_elements_to_show) 7052 gui_utils.hide_gui_elements(gui_elements_to_hide) 7053 prot_1_name = self._view.ui.lbl_pred_analysis_multi_prot_struct_1.text() 7054 prot_1_chains = [] 7055 for chain in self._view.ui.list_pred_analysis_multi_ref_chains.selectedItems(): 7056 prot_1_chains.append(chain.text()) 7057 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 7058 prot_2_name = self._view.ui.lbl_pred_analysis_multi_prot_struct_2.text() 7059 prot_2_chains = [] 7060 for chain in self._view.ui.list_pred_analysis_multi_model_chains.selectedItems(): 7061 prot_2_chains.append(chain.text()) 7062 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 7063 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 7064 item = QtWidgets.QListWidgetItem(analysis_name) 7065 self._view.ui.list_pred_analysis_multi_overview.addItem(item) 7066 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(False)
Adds the protein pair to the list of protein pairs to analyze.
def
multi_pred_analysis_structure_analysis_back_5(self) -> None:
7068 def multi_pred_analysis_structure_analysis_back_5(self) -> None: 7069 """Hides the gui elements to select the chains in protein 2.""" 7070 gui_elements_to_show = [ 7071 self._view.ui.lbl_pred_analysis_multi_overview, 7072 self._view.ui.list_pred_analysis_multi_overview, 7073 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 7074 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 7075 self._view.ui.lbl_analysis_batch_vs_3, 7076 self._view.ui.lbl_pred_analysis_multi_ref_chains, 7077 self._view.ui.list_pred_analysis_multi_ref_chains, 7078 self._view.ui.btn_pred_analysis_multi_back_4, 7079 self._view.ui.btn_pred_analysis_multi_next_3, 7080 ] 7081 gui_elements_to_hide = [ 7082 self._view.ui.btn_pred_analysis_multi_remove, 7083 self._view.ui.btn_pred_analysis_multi_add, 7084 self._view.ui.box_pred_analysis_multi_prot_struct_1, 7085 self._view.ui.box_pred_analysis_multi_prot_struct_2, 7086 self._view.ui.btn_pred_analysis_multi_back_3, 7087 self._view.ui.btn_pred_analysis_multi_next_2, 7088 self._view.ui.btn_pred_analysis_multi_back_5, 7089 self._view.ui.btn_pred_analysis_multi_next_4, 7090 self._view.ui.lbl_pred_analysis_multi_images, 7091 self._view.ui.cb_pred_analysis_multi_images, 7092 self._view.ui.btn_pred_analysis_multi_start, 7093 self._view.ui.lbl_pred_analysis_multi_model_chains, 7094 self._view.ui.list_pred_analysis_multi_model_chains, 7095 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 7096 ] 7097 gui_utils.show_gui_elements(gui_elements_to_show) 7098 gui_utils.hide_gui_elements(gui_elements_to_hide) 7099 self._view.ui.list_pred_analysis_multi_ref_chains.setEnabled(True) 7100 7101 # tmp_protein = self._current_project.search_protein(self._view.ui.box_pred_analysis_multi_prot_struct_2.currentText()) 7102 # for tmp_chain in tmp_protein.chains: 7103 # if tmp_chain.chain_type == "protein_chain": 7104 # self._view.ui.list_pred_analysis_multi_ref_chains.addItem(tmp_chain.chain_letter)
Hides the gui elements to select the chains in protein 2.
def
multi_pred_analysis_structure_analysis_overview_clicked(self) -> None:
7106 def multi_pred_analysis_structure_analysis_overview_clicked(self) -> None: 7107 """Enables the remove button.""" 7108 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(True)
Enables the remove button.
def
fill_multi_pred_analysis_protein_boxes(self) -> None:
7110 def fill_multi_pred_analysis_protein_boxes(self) -> None: 7111 """Fills the combo boxes with the protein names.""" 7112 protein_names = [] 7113 for i in range(self._view.ui.table_pred_analysis_multi_prot_to_predict.rowCount()): 7114 protein_names.append(self._view.ui.table_pred_analysis_multi_prot_to_predict.verticalHeaderItem(i).text()) 7115 for tmp_protein in self._current_project.proteins: 7116 protein_names.append(tmp_protein.get_molecule_object()) 7117 protein_names.insert(0, "") 7118 protein_names = list(set(protein_names)) 7119 self._view.ui.box_pred_analysis_multi_prot_struct_1.clear() 7120 self._view.ui.box_pred_analysis_multi_prot_struct_2.clear() 7121 gui_utils.fill_combo_box(self._view.ui.box_pred_analysis_multi_prot_struct_1, protein_names) 7122 gui_utils.fill_combo_box(self._view.ui.box_pred_analysis_multi_prot_struct_2, protein_names)
Fills the combo boxes with the protein names.
def
remove_multi_pred_analysis_analysis_run(self) -> None:
7124 def remove_multi_pred_analysis_analysis_run(self) -> None: 7125 """Removes the selected protein pair from the list of protein pairs to analyze.""" 7126 self._view.ui.list_pred_analysis_multi_overview.takeItem( 7127 self._view.ui.list_pred_analysis_multi_overview.currentRow(), 7128 ) 7129 gui_elements_to_show = [ 7130 self._view.ui.lbl_pred_analysis_multi_overview, 7131 self._view.ui.list_pred_analysis_multi_overview, 7132 self._view.ui.btn_pred_analysis_multi_add, 7133 self._view.ui.btn_pred_analysis_multi_back_pred_setup, 7134 ] 7135 gui_elements_to_hide = [ 7136 self._view.ui.btn_pred_analysis_multi_remove, 7137 self._view.ui.lbl_pred_analysis_multi_prot_struct_1, 7138 self._view.ui.lbl_pred_analysis_multi_prot_struct_2, 7139 self._view.ui.lbl_analysis_batch_vs_3, 7140 self._view.ui.lbl_pred_analysis_multi_ref_chains, 7141 self._view.ui.list_pred_analysis_multi_ref_chains, 7142 self._view.ui.btn_pred_analysis_multi_back_4, 7143 self._view.ui.btn_pred_analysis_multi_next_3, 7144 self._view.ui.box_pred_analysis_multi_prot_struct_1, 7145 self._view.ui.box_pred_analysis_multi_prot_struct_2, 7146 self._view.ui.btn_pred_analysis_multi_back_3, 7147 self._view.ui.btn_pred_analysis_multi_next_2, 7148 self._view.ui.lbl_pred_analysis_multi_model_chains, 7149 self._view.ui.list_pred_analysis_multi_model_chains, 7150 self._view.ui.btn_pred_analysis_multi_back_5, 7151 self._view.ui.btn_pred_analysis_multi_next_4, 7152 self._view.ui.lbl_pred_analysis_multi_images, 7153 self._view.ui.cb_pred_analysis_multi_images, 7154 self._view.ui.btn_pred_analysis_multi_start, 7155 ] 7156 gui_utils.show_gui_elements(gui_elements_to_show) 7157 gui_utils.hide_gui_elements(gui_elements_to_hide) 7158 if self._view.ui.list_pred_analysis_multi_overview.count() > 0: 7159 self._view.ui.btn_pred_analysis_multi_remove.show() 7160 self._view.ui.btn_pred_analysis_multi_remove.setEnabled(False) 7161 self._view.ui.btn_pred_analysis_multi_start.show() 7162 self._view.ui.lbl_pred_analysis_multi_images.show() 7163 self._view.ui.cb_pred_analysis_multi_images.show() 7164 # if self._view.ui.list_pred_analysis_multi_overview.count() == 0: 7165 # 7166 # self._view.ui.btn_pred_analysis_multi_back_pred_setup.show() 7167 # self._view.ui.btn_pred_analysis_multi_remove.hide()
Removes the selected protein pair from the list of protein pairs to analyze.
def
check_multi_pred_analysis_if_same_no_of_chains_selected(self) -> None:
7169 def check_multi_pred_analysis_if_same_no_of_chains_selected(self) -> None: 7170 """Checks if the same number of chains were selected.""" 7171 self._view.ui.btn_pred_analysis_multi_next_4.setEnabled(False) 7172 if self.no_of_selected_chains == len(self._view.ui.list_pred_analysis_multi_model_chains.selectedItems()): 7173 self._view.ui.btn_pred_analysis_multi_next_4.setEnabled(True) 7174 7175 prot_1_name = self._view.ui.lbl_pred_analysis_multi_prot_struct_1.text() 7176 prot_1_chains = [] 7177 for chain in self._view.ui.list_pred_analysis_multi_ref_chains.selectedItems(): 7178 prot_1_chains.append(chain.text()) 7179 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 7180 prot_2_name = self._view.ui.lbl_pred_analysis_multi_prot_struct_2.text() 7181 prot_2_chains = [] 7182 for chain in self._view.ui.list_pred_analysis_multi_model_chains.selectedItems(): 7183 prot_2_chains.append(chain.text()) 7184 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 7185 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 7186 for tmp_row in range(self._view.ui.list_pred_analysis_multi_overview.count()): 7187 if analysis_name == self._view.ui.list_pred_analysis_multi_overview.item(tmp_row).text(): 7188 self._view.ui.btn_pred_analysis_multi_next_4.setEnabled(False) 7189 styles.color_button_not_ready(self._view.ui.btn_pred_analysis_multi_next_4) 7190 return
Checks if the same number of chains were selected.
def
check_multi_pred_analysis_if_prot_structs_are_filled(self) -> None:
7192 def check_multi_pred_analysis_if_prot_structs_are_filled(self) -> None: 7193 """Checks if two proteins were selected.""" 7194 prot_1 = self._view.ui.box_pred_analysis_multi_prot_struct_1.itemText( 7195 self._view.ui.box_pred_analysis_multi_prot_struct_1.currentIndex(), 7196 ) 7197 prot_2 = self._view.ui.box_pred_analysis_multi_prot_struct_2.itemText( 7198 self._view.ui.box_pred_analysis_multi_prot_struct_2.currentIndex(), 7199 ) 7200 if prot_1 != "" and prot_2 != "": 7201 self._view.ui.btn_pred_analysis_multi_next_2.setEnabled(True) 7202 else: 7203 self._view.ui.btn_pred_analysis_multi_next_2.setEnabled(False)
Checks if two proteins were selected.
def
count_multi_pred_analysis_selected_chains_for_prot_struct_1(self) -> None:
7205 def count_multi_pred_analysis_selected_chains_for_prot_struct_1(self) -> None: 7206 """Counts the number of chains in protein 1.""" 7207 self.no_of_selected_chains = len(self._view.ui.list_pred_analysis_multi_ref_chains.selectedItems()) 7208 if self.no_of_selected_chains > 0: 7209 self._view.ui.btn_pred_analysis_multi_next_3.setEnabled(True) 7210 else: 7211 self._view.ui.btn_pred_analysis_multi_next_3.setEnabled(False)
Counts the number of chains in protein 1.
def
structure_analysis_add(self) -> None:
7217 def structure_analysis_add(self) -> None: 7218 """Shows the gui elements to choose the two proteins.""" 7219 gui_elements_to_show = [ 7220 self._view.ui.lbl_analysis_batch_overview, 7221 self._view.ui.list_analysis_batch_overview, 7222 self._view.ui.lbl_analysis_batch_prot_struct_1, 7223 self._view.ui.box_analysis_batch_prot_struct_1, 7224 self._view.ui.lbl_analysis_batch_vs, 7225 self._view.ui.lbl_analysis_batch_prot_struct_2, 7226 self._view.ui.box_analysis_batch_prot_struct_2, 7227 self._view.ui.btn_analysis_batch_back, 7228 self._view.ui.btn_analysis_batch_next, 7229 ] 7230 gui_elements_to_hide = [ 7231 self._view.ui.btn_analysis_batch_remove, 7232 self._view.ui.btn_analysis_batch_add, 7233 self._view.ui.lbl_analysis_batch_ref_chains, 7234 self._view.ui.list_analysis_batch_ref_chains, 7235 self._view.ui.btn_analysis_batch_back_2, 7236 self._view.ui.btn_analysis_batch_next_2, 7237 self._view.ui.lbl_analysis_batch_model_chains, 7238 self._view.ui.list_analysis_batch_model_chains, 7239 self._view.ui.btn_analysis_batch_back_3, 7240 self._view.ui.btn_analysis_batch_next_3, 7241 self._view.ui.lbl_analysis_batch_images, 7242 self._view.ui.cb_analysis_batch_images, 7243 self._view.ui.btn_analysis_batch_start, 7244 ] 7245 7246 gui_utils.show_gui_elements(gui_elements_to_show) 7247 gui_utils.hide_gui_elements(gui_elements_to_hide) 7248 self._view.ui.lbl_analysis_batch_prot_struct_1.clear() 7249 self._view.ui.lbl_analysis_batch_prot_struct_2.clear() 7250 self._view.ui.lbl_analysis_batch_prot_struct_1.setText("Protein structure 1") 7251 self._view.ui.lbl_analysis_batch_prot_struct_2.setText("Protein structure 2") 7252 self.fill_protein_boxes_batch() 7253 if self._view.ui.list_analysis_batch_overview.count() > 0: 7254 try: 7255 self._view.ui.list_analysis_batch_overview.currentItem().setSelected(False) 7256 except AttributeError: 7257 constants.PYSSA_LOGGER.debug("No selection in struction analysis overview.")
Shows the gui elements to choose the two proteins.
def
structure_analysis_back(self) -> None:
7259 def structure_analysis_back(self) -> None: 7260 """Hides the gui elements to choose the two proteins.""" 7261 gui_elements_to_show = [ 7262 self._view.ui.lbl_analysis_batch_overview, 7263 self._view.ui.list_analysis_batch_overview, 7264 self._view.ui.btn_analysis_batch_add, 7265 ] 7266 gui_elements_to_hide = [ 7267 self._view.ui.btn_analysis_batch_remove, 7268 self._view.ui.lbl_analysis_batch_prot_struct_1, 7269 self._view.ui.lbl_analysis_batch_prot_struct_2, 7270 self._view.ui.lbl_analysis_batch_vs, 7271 self._view.ui.lbl_analysis_batch_ref_chains, 7272 self._view.ui.list_analysis_batch_ref_chains, 7273 self._view.ui.btn_analysis_batch_back_2, 7274 self._view.ui.btn_analysis_batch_next_2, 7275 self._view.ui.box_analysis_batch_prot_struct_1, 7276 self._view.ui.box_analysis_batch_prot_struct_2, 7277 self._view.ui.btn_analysis_batch_back, 7278 self._view.ui.btn_analysis_batch_next, 7279 self._view.ui.lbl_analysis_batch_model_chains, 7280 self._view.ui.list_analysis_batch_model_chains, 7281 self._view.ui.btn_analysis_batch_back_3, 7282 self._view.ui.btn_analysis_batch_next_3, 7283 self._view.ui.lbl_analysis_batch_images, 7284 self._view.ui.cb_analysis_batch_images, 7285 self._view.ui.btn_analysis_batch_start, 7286 ] 7287 gui_utils.show_gui_elements(gui_elements_to_show) 7288 gui_utils.hide_gui_elements(gui_elements_to_hide) 7289 if self._view.ui.list_analysis_batch_overview.count() > 0: 7290 self._view.ui.btn_analysis_batch_remove.show() 7291 self._view.ui.btn_analysis_batch_remove.setEnabled(False) 7292 self._view.ui.btn_analysis_batch_start.show() 7293 self._view.ui.lbl_analysis_batch_images.show() 7294 self._view.ui.cb_analysis_batch_images.show()
Hides the gui elements to choose the two proteins.
def
structure_analysis_next_2(self) -> None:
7296 def structure_analysis_next_2(self) -> None: 7297 """Shows the gui elements to select the chains in protein 2.""" 7298 gui_elements_to_show = [ 7299 self._view.ui.lbl_analysis_batch_overview, 7300 self._view.ui.list_analysis_batch_overview, 7301 self._view.ui.lbl_analysis_batch_prot_struct_1, 7302 self._view.ui.lbl_analysis_batch_prot_struct_2, 7303 self._view.ui.lbl_analysis_batch_vs, 7304 self._view.ui.lbl_analysis_batch_ref_chains, 7305 self._view.ui.list_analysis_batch_ref_chains, 7306 self._view.ui.lbl_analysis_batch_model_chains, 7307 self._view.ui.list_analysis_batch_model_chains, 7308 self._view.ui.btn_analysis_batch_back_3, 7309 self._view.ui.btn_analysis_batch_next_3, 7310 ] 7311 gui_elements_to_hide = [ 7312 self._view.ui.btn_analysis_batch_remove, 7313 self._view.ui.btn_analysis_batch_add, 7314 self._view.ui.box_analysis_batch_prot_struct_1, 7315 self._view.ui.box_analysis_batch_prot_struct_2, 7316 self._view.ui.btn_analysis_batch_back, 7317 self._view.ui.btn_analysis_batch_next, 7318 self._view.ui.btn_analysis_batch_back_2, 7319 self._view.ui.btn_analysis_batch_next_2, 7320 self._view.ui.lbl_analysis_batch_images, 7321 self._view.ui.cb_analysis_batch_images, 7322 self._view.ui.btn_analysis_batch_start, 7323 ] 7324 gui_utils.show_gui_elements(gui_elements_to_show) 7325 gui_utils.hide_gui_elements(gui_elements_to_hide) 7326 self._view.ui.list_analysis_batch_model_chains.clear() 7327 self._view.ui.list_analysis_batch_ref_chains.setEnabled(False) 7328 self._view.ui.btn_analysis_batch_next_3.setEnabled(False) 7329 7330 tmp_protein = self._current_project.search_protein(self._view.ui.box_analysis_batch_prot_struct_2.currentText()) 7331 for tmp_chain in tmp_protein.chains: 7332 if tmp_chain.chain_type == "protein_chain": 7333 self._view.ui.list_analysis_batch_model_chains.addItem(tmp_chain.chain_letter) 7334 if len(self._view.ui.list_analysis_batch_ref_chains.selectedItems()) == 1: 7335 self._view.ui.lbl_analysis_batch_model_chains.setText( 7336 f"Select 1 chain in protein structure {self._view.ui.lbl_analysis_batch_prot_struct_2.text()}.", 7337 ) 7338 else: 7339 self._view.ui.lbl_analysis_batch_model_chains.setText( 7340 f"Select {len(self._view.ui.list_analysis_batch_ref_chains.selectedItems())} chains in " 7341 f"protein structure {self._view.ui.lbl_analysis_batch_prot_struct_2.text()}.", 7342 )
Shows the gui elements to select the chains in protein 2.
def
structure_analysis_back_2(self) -> None:
7344 def structure_analysis_back_2(self) -> None: 7345 """Hides the gui elements to select the chains in protein 1.""" 7346 gui_elements_to_show = [ 7347 self._view.ui.lbl_analysis_batch_overview, 7348 self._view.ui.list_analysis_batch_overview, 7349 self._view.ui.lbl_analysis_batch_prot_struct_1, 7350 self._view.ui.box_analysis_batch_prot_struct_1, 7351 self._view.ui.lbl_analysis_batch_vs, 7352 self._view.ui.lbl_analysis_batch_prot_struct_2, 7353 self._view.ui.box_analysis_batch_prot_struct_2, 7354 self._view.ui.btn_analysis_batch_back, 7355 self._view.ui.btn_analysis_batch_next, 7356 ] 7357 gui_elements_to_hide = [ 7358 self._view.ui.btn_analysis_batch_remove, 7359 self._view.ui.btn_analysis_batch_add, 7360 self._view.ui.lbl_analysis_batch_ref_chains, 7361 self._view.ui.list_analysis_batch_ref_chains, 7362 self._view.ui.btn_analysis_batch_back_2, 7363 self._view.ui.btn_analysis_batch_next_2, 7364 self._view.ui.lbl_analysis_batch_model_chains, 7365 self._view.ui.list_analysis_batch_model_chains, 7366 self._view.ui.btn_analysis_batch_back_3, 7367 self._view.ui.btn_analysis_batch_next_3, 7368 self._view.ui.lbl_analysis_batch_images, 7369 self._view.ui.cb_analysis_batch_images, 7370 self._view.ui.btn_analysis_batch_start, 7371 ] 7372 gui_utils.show_gui_elements(gui_elements_to_show) 7373 gui_utils.hide_gui_elements(gui_elements_to_hide) 7374 self._view.ui.lbl_analysis_batch_prot_struct_1.setText("Protein structure 1") 7375 self._view.ui.lbl_analysis_batch_prot_struct_2.setText("Protein structure 2")
Hides the gui elements to select the chains in protein 1.
def
structure_analysis_next_3(self) -> None:
7377 def structure_analysis_next_3(self) -> None: 7378 """Adds the protein pair to the list of protein pairs to analyze.""" 7379 gui_elements_to_show = [ 7380 self._view.ui.btn_analysis_batch_remove, 7381 self._view.ui.btn_analysis_batch_add, 7382 self._view.ui.lbl_analysis_batch_overview, 7383 self._view.ui.list_analysis_batch_overview, 7384 self._view.ui.lbl_analysis_batch_images, 7385 self._view.ui.cb_analysis_batch_images, 7386 self._view.ui.btn_analysis_batch_start, 7387 ] 7388 gui_elements_to_hide = [ 7389 self._view.ui.box_analysis_batch_prot_struct_1, 7390 self._view.ui.box_analysis_batch_prot_struct_2, 7391 self._view.ui.lbl_analysis_batch_prot_struct_1, 7392 self._view.ui.lbl_analysis_batch_prot_struct_2, 7393 self._view.ui.lbl_analysis_batch_vs, 7394 self._view.ui.lbl_analysis_batch_ref_chains, 7395 self._view.ui.list_analysis_batch_ref_chains, 7396 self._view.ui.lbl_analysis_batch_model_chains, 7397 self._view.ui.list_analysis_batch_model_chains, 7398 self._view.ui.btn_analysis_batch_back, 7399 self._view.ui.btn_analysis_batch_next, 7400 self._view.ui.btn_analysis_batch_back_2, 7401 self._view.ui.btn_analysis_batch_next_2, 7402 self._view.ui.btn_analysis_batch_back_3, 7403 self._view.ui.btn_analysis_batch_next_3, 7404 ] 7405 gui_utils.show_gui_elements(gui_elements_to_show) 7406 gui_utils.hide_gui_elements(gui_elements_to_hide) 7407 prot_1_name = self._view.ui.lbl_analysis_batch_prot_struct_1.text() 7408 prot_1_chains = [] 7409 for chain in self._view.ui.list_analysis_batch_ref_chains.selectedItems(): 7410 prot_1_chains.append(chain.text()) 7411 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 7412 prot_2_name = self._view.ui.lbl_analysis_batch_prot_struct_2.text() 7413 prot_2_chains = [] 7414 for chain in self._view.ui.list_analysis_batch_model_chains.selectedItems(): 7415 prot_2_chains.append(chain.text()) 7416 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 7417 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 7418 item = QtWidgets.QListWidgetItem(analysis_name) 7419 self._view.ui.list_analysis_batch_overview.addItem(item) 7420 self._view.ui.btn_analysis_batch_remove.setEnabled(False)
Adds the protein pair to the list of protein pairs to analyze.
def
structure_analysis_back_3(self) -> None:
7422 def structure_analysis_back_3(self) -> None: 7423 """Hides the gui elements to select the chains in protein 2.""" 7424 gui_elements_to_show = [ 7425 self._view.ui.lbl_analysis_batch_overview, 7426 self._view.ui.list_analysis_batch_overview, 7427 self._view.ui.lbl_analysis_batch_prot_struct_1, 7428 self._view.ui.lbl_analysis_batch_prot_struct_2, 7429 self._view.ui.lbl_analysis_batch_vs, 7430 self._view.ui.lbl_analysis_batch_ref_chains, 7431 self._view.ui.list_analysis_batch_ref_chains, 7432 self._view.ui.btn_analysis_batch_back_2, 7433 self._view.ui.btn_analysis_batch_next_2, 7434 ] 7435 gui_elements_to_hide = [ 7436 self._view.ui.btn_analysis_batch_remove, 7437 self._view.ui.btn_analysis_batch_add, 7438 self._view.ui.box_analysis_batch_prot_struct_1, 7439 self._view.ui.box_analysis_batch_prot_struct_2, 7440 self._view.ui.btn_analysis_batch_back, 7441 self._view.ui.btn_analysis_batch_next, 7442 self._view.ui.btn_analysis_batch_back_3, 7443 self._view.ui.btn_analysis_batch_next_3, 7444 self._view.ui.lbl_analysis_batch_images, 7445 self._view.ui.cb_analysis_batch_images, 7446 self._view.ui.btn_analysis_batch_start, 7447 self._view.ui.lbl_analysis_batch_model_chains, 7448 self._view.ui.list_analysis_batch_model_chains, 7449 ] 7450 gui_utils.show_gui_elements(gui_elements_to_show) 7451 gui_utils.hide_gui_elements(gui_elements_to_hide) 7452 self._view.ui.list_analysis_batch_ref_chains.setEnabled(True) 7453 7454 # tmp_protein = self._current_project.search_protein(self._view.ui.box_analysis_batch_prot_struct_2.currentText()) 7455 # for tmp_chain in tmp_protein.chains: 7456 # if tmp_chain.chain_type == "protein_chain": 7457 # self._view.ui.list_analysis_batch_ref_chains.addItem(tmp_chain.chain_letter)
Hides the gui elements to select the chains in protein 2.
def
structure_analysis_overview_clicked(self) -> None:
7459 def structure_analysis_overview_clicked(self) -> None: 7460 """Enables the remove button.""" 7461 self._view.ui.btn_analysis_batch_remove.setEnabled(True)
Enables the remove button.
def
fill_protein_boxes_batch(self) -> None:
7463 def fill_protein_boxes_batch(self) -> None: 7464 """Fills the combo boxes with the protein names.""" 7465 proteins = [] 7466 for tmp_protein in self._current_project.proteins: 7467 proteins.append(tmp_protein.get_molecule_object()) 7468 proteins.insert(0, "") 7469 self._view.ui.box_analysis_batch_prot_struct_1.clear() 7470 self._view.ui.box_analysis_batch_prot_struct_2.clear() 7471 gui_utils.fill_combo_box(self._view.ui.box_analysis_batch_prot_struct_1, proteins) 7472 gui_utils.fill_combo_box(self._view.ui.box_analysis_batch_prot_struct_2, proteins)
Fills the combo boxes with the protein names.
def
remove_analysis_run(self) -> None:
7474 def remove_analysis_run(self) -> None: 7475 """Removes the selected protein pair from the list of protein pairs to analyze.""" 7476 self._view.ui.list_analysis_batch_overview.takeItem(self._view.ui.list_analysis_batch_overview.currentRow()) 7477 if self._view.ui.list_analysis_batch_overview.count() == 0: 7478 gui_elements_to_show = [ 7479 self._view.ui.lbl_analysis_batch_overview, 7480 self._view.ui.list_analysis_batch_overview, 7481 self._view.ui.btn_analysis_batch_add, 7482 ] 7483 7484 gui_elements_to_hide = [ 7485 self._view.ui.btn_analysis_batch_remove, 7486 self._view.ui.lbl_analysis_batch_prot_struct_1, 7487 self._view.ui.lbl_analysis_batch_prot_struct_2, 7488 self._view.ui.lbl_analysis_batch_vs, 7489 self._view.ui.lbl_analysis_batch_ref_chains, 7490 self._view.ui.list_analysis_batch_ref_chains, 7491 self._view.ui.btn_analysis_batch_back_2, 7492 self._view.ui.btn_analysis_batch_next_2, 7493 self._view.ui.box_analysis_batch_prot_struct_1, 7494 self._view.ui.box_analysis_batch_prot_struct_2, 7495 self._view.ui.btn_analysis_batch_back, 7496 self._view.ui.btn_analysis_batch_next, 7497 self._view.ui.lbl_analysis_batch_model_chains, 7498 self._view.ui.list_analysis_batch_model_chains, 7499 self._view.ui.btn_analysis_batch_back_3, 7500 self._view.ui.btn_analysis_batch_next_3, 7501 self._view.ui.lbl_analysis_batch_images, 7502 self._view.ui.cb_analysis_batch_images, 7503 self._view.ui.btn_analysis_batch_start, 7504 ] 7505 7506 gui_utils.show_gui_elements(gui_elements_to_show) 7507 gui_utils.hide_gui_elements(gui_elements_to_hide) 7508 self._view.ui.btn_analysis_batch_remove.hide() 7509 else: 7510 if self._view.ui.list_analysis_batch_overview.count() > 0: 7511 try: 7512 self._view.ui.list_analysis_batch_overview.currentItem().setSelected(False) 7513 except AttributeError: 7514 constants.PYSSA_LOGGER.debug("No selection in struction analysis overview.") 7515 self._view.ui.btn_analysis_batch_remove.setEnabled(False)
Removes the selected protein pair from the list of protein pairs to analyze.
def
check_if_same_no_of_chains_selected_batch(self) -> None:
7517 def check_if_same_no_of_chains_selected_batch(self) -> None: 7518 """Checks if the same number of proteins were selected.""" 7519 self._view.ui.btn_analysis_batch_next_3.setEnabled(False) 7520 if self.no_of_selected_chains == len(self._view.ui.list_analysis_batch_model_chains.selectedItems()): 7521 self._view.ui.btn_analysis_batch_next_3.setEnabled(True) 7522 7523 prot_1_name = self._view.ui.lbl_analysis_batch_prot_struct_1.text() 7524 prot_1_chains = [] 7525 for chain in self._view.ui.list_analysis_batch_ref_chains.selectedItems(): 7526 prot_1_chains.append(chain.text()) 7527 prot_1_chains = ",".join([str(elem) for elem in prot_1_chains]) 7528 prot_2_name = self._view.ui.lbl_analysis_batch_prot_struct_2.text() 7529 prot_2_chains = [] 7530 for chain in self._view.ui.list_analysis_batch_model_chains.selectedItems(): 7531 prot_2_chains.append(chain.text()) 7532 prot_2_chains = ",".join([str(elem) for elem in prot_2_chains]) 7533 analysis_name = f"{prot_1_name};{prot_1_chains}_vs_{prot_2_name};{prot_2_chains}" 7534 for tmp_row in range(self._view.ui.list_analysis_batch_overview.count()): 7535 if analysis_name == self._view.ui.list_analysis_batch_overview.item(tmp_row).text(): 7536 self._view.ui.btn_analysis_batch_next_3.setEnabled(False) 7537 styles.color_button_not_ready(self._view.ui.btn_analysis_batch_next_3) 7538 return
Checks if the same number of proteins were selected.
def
check_if_prot_structs_are_filled_batch(self) -> None:
7540 def check_if_prot_structs_are_filled_batch(self) -> None: 7541 """Checks if two proteins were selected.""" 7542 prot_1 = self._view.ui.box_analysis_batch_prot_struct_1.itemText( 7543 self._view.ui.box_analysis_batch_prot_struct_1.currentIndex(), 7544 ) 7545 prot_2 = self._view.ui.box_analysis_batch_prot_struct_2.itemText( 7546 self._view.ui.box_analysis_batch_prot_struct_2.currentIndex(), 7547 ) 7548 if prot_1 != "" and prot_2 != "": 7549 self._view.ui.btn_analysis_batch_next.setEnabled(True) 7550 else: 7551 self._view.ui.btn_analysis_batch_next.setEnabled(False)
Checks if two proteins were selected.
def
count_batch_selected_chains_for_prot_struct_1(self) -> None:
7553 def count_batch_selected_chains_for_prot_struct_1(self) -> None: 7554 """Counts the number of chains of protein 1.""" 7555 self.no_of_selected_chains = len(self._view.ui.list_analysis_batch_ref_chains.selectedItems()) 7556 if self.no_of_selected_chains > 0: 7557 self._view.ui.btn_analysis_batch_next_2.setEnabled(True) 7558 else: 7559 self._view.ui.btn_analysis_batch_next_2.setEnabled(False)
Counts the number of chains of protein 1.
def
display_image_analysis_page(self) -> None:
7564 def display_image_analysis_page(self) -> None: 7565 """Displays the analysis image work area.""" 7566 # get all protein pairs without images 7567 self._view.ui.list_analysis_images_struct_analysis.clear() 7568 self._view.ui.list_analysis_images_creation_struct_analysis.clear() 7569 for tmp_protein_pair in self._current_project.protein_pairs: 7570 if len(tmp_protein_pair.distance_analysis.analysis_results.structure_aln_image) == 0: 7571 self._view.ui.list_analysis_images_struct_analysis.addItem(tmp_protein_pair.name) 7572 self.last_sidebar_button = styles.color_sidebar_buttons( 7573 self.last_sidebar_button, 7574 self._view.ui.btn_image_analysis_page, 7575 ) 7576 tools.switch_page(self._view.ui.stackedWidget, self._view.ui.lbl_page_title, 23, "Analysis Images") 7577 self._view.ui.btn_add_analysis_images_struct_analysis.setEnabled(False) 7578 self._view.ui.btn_remove_analysis_images_creation_struct_analysis.setEnabled(False) 7579 self._view.ui.btn_start_automatic_image_creation.setEnabled(False)
Displays the analysis image work area.
def
analysis_images_enable_add(self) -> None:
7581 def analysis_images_enable_add(self) -> None: 7582 """Enables the add button.""" 7583 self._view.ui.btn_add_analysis_images_struct_analysis.setEnabled(True)
Enables the add button.
def
analysis_images_enable_remove(self) -> None:
7585 def analysis_images_enable_remove(self) -> None: 7586 """Enables the remove button.""" 7587 self._view.ui.btn_remove_analysis_images_creation_struct_analysis.setEnabled(True)
Enables the remove button.
def
add_protein_pair_to_image_creation_queue(self) -> None:
7589 def add_protein_pair_to_image_creation_queue(self) -> None: 7590 """Adds a protein pair from the list of protein pairs to make images of.""" 7591 protein_pair_to_add = self._view.ui.list_analysis_images_struct_analysis.currentItem().text() 7592 self._view.ui.list_analysis_images_creation_struct_analysis.addItem(protein_pair_to_add) 7593 self._view.ui.list_analysis_images_struct_analysis.takeItem( 7594 self._view.ui.list_analysis_images_struct_analysis.currentRow(), 7595 ) 7596 self._view.ui.btn_add_analysis_images_struct_analysis.setEnabled(False) 7597 self.analysis_images_check_if_creation_can_start()
Adds a protein pair from the list of protein pairs to make images of.
def
remove_protein_pair_from_image_creation_queue(self) -> None:
7599 def remove_protein_pair_from_image_creation_queue(self) -> None: 7600 """Removes a protein pair from the list of protein pairs to make images of.""" 7601 protein_pair_to_remove = self._view.ui.list_analysis_images_creation_struct_analysis.currentItem() 7602 self._view.ui.list_analysis_images_creation_struct_analysis.takeItem( 7603 self._view.ui.list_analysis_images_creation_struct_analysis.currentRow(), 7604 ) 7605 self._view.ui.list_analysis_images_struct_analysis.addItem(protein_pair_to_remove) 7606 self._view.ui.btn_remove_analysis_images_creation_struct_analysis.setEnabled(False) 7607 self.analysis_images_check_if_creation_can_start()
Removes a protein pair from the list of protein pairs to make images of.
def
analysis_images_check_if_creation_can_start(self) -> None:
7609 def analysis_images_check_if_creation_can_start(self) -> None: 7610 """Checks if the list of protein pairs which get images are empty.""" 7611 if self._view.ui.list_analysis_images_creation_struct_analysis.count() > 0: 7612 self._view.ui.btn_start_automatic_image_creation.setEnabled(True) 7613 else: 7614 self._view.ui.btn_start_automatic_image_creation.setEnabled(False)
Checks if the list of protein pairs which get images are empty.